[galaxy-dev] Elastic Bean Stalk
Hi all - I was wondering, if we deploy Galaxy in AWS, can we take advantage of Elastic BeanStalk to scale our instances based on demand instead of trying to configure Galaxy to perform well for our users? Ryan ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Converting an internal user to an external user
Ok I got it. I had to update the email address field to match what the REMOTE_USER variable was being set my Apache. On Wed, Sep 7, 2016 at 1:41 PM, Ryan G wrote: > Sorry, missed your other questions... > > external authentication via apache...yes. Its working well for us. > The userid is the same. I'm clearly missing something. I need to find > in the code where this is and add some debugging statements. > > On Wed, Sep 7, 2016 at 12:15 PM, Hans-Rudolf Hotz wrote: > >> Hi Ryan >> >> Are you doing external authentication via apache? >> >> if so, I suggest to change the value in the 'external' column from 'f' to >> 't' in the galaxy_user table. >> >> also, check, whether the e-mail used is really the same as the one coming >> from your external authentication system. >> >> However, be very careful, whenever you manually interact with the Galaxy >> PostgreSQL database. Make sure you have an up-to-date back-up. >> >> Hope this helps, >> Hans-Rudolf >> >> >> >> >> On 09/07/2016 05:27 PM, Ryan G wrote: >> >>> Hi all - I'm having a problem with a user account and Galaxy getting >>> confused with it being internal vs external. >>> >>> When we first set up galaxy, we were using Galaxy's internal >>> authentication system. This worked well but all our users then had >>> another password to keep track of. >>> >>> We activated external user authentication a few months ago and it works >>> fine for us. >>> >>> This user hasn't logged in since and recently tried but is unable to. >>> >>> I discovered her account in Galaxy appears as an internal account eg >>> created before we were using external authentication. Now that we have >>> external authentication, Galaxy doesn't recognize her and she gets the >>> user_disabled page whenever she tries to log in. >>> >>> Is there a way I can change her account in Galaxy from being an internal >>> to an external account? >>> >>> Ryan >>> >>> >>> ___ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>>https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>>http://galaxyproject.org/search/mailinglists/ >>> >>> > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Converting an internal user to an external user
Sorry, missed your other questions... external authentication via apache...yes. Its working well for us. The userid is the same. I'm clearly missing something. I need to find in the code where this is and add some debugging statements. On Wed, Sep 7, 2016 at 12:15 PM, Hans-Rudolf Hotz wrote: > Hi Ryan > > Are you doing external authentication via apache? > > if so, I suggest to change the value in the 'external' column from 'f' to > 't' in the galaxy_user table. > > also, check, whether the e-mail used is really the same as the one coming > from your external authentication system. > > However, be very careful, whenever you manually interact with the Galaxy > PostgreSQL database. Make sure you have an up-to-date back-up. > > Hope this helps, > Hans-Rudolf > > > > > On 09/07/2016 05:27 PM, Ryan G wrote: > >> Hi all - I'm having a problem with a user account and Galaxy getting >> confused with it being internal vs external. >> >> When we first set up galaxy, we were using Galaxy's internal >> authentication system. This worked well but all our users then had >> another password to keep track of. >> >> We activated external user authentication a few months ago and it works >> fine for us. >> >> This user hasn't logged in since and recently tried but is unable to. >> >> I discovered her account in Galaxy appears as an internal account eg >> created before we were using external authentication. Now that we have >> external authentication, Galaxy doesn't recognize her and she gets the >> user_disabled page whenever she tries to log in. >> >> Is there a way I can change her account in Galaxy from being an internal >> to an external account? >> >> Ryan >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >>https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >>http://galaxyproject.org/search/mailinglists/ >> >> ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Converting an internal user to an external user
Hi all - I'm having a problem with a user account and Galaxy getting confused with it being internal vs external. When we first set up galaxy, we were using Galaxy's internal authentication system. This worked well but all our users then had another password to keep track of. We activated external user authentication a few months ago and it works fine for us. This user hasn't logged in since and recently tried but is unable to. I discovered her account in Galaxy appears as an internal account eg created before we were using external authentication. Now that we have external authentication, Galaxy doesn't recognize her and she gets the user_disabled page whenever she tries to log in. Is there a way I can change her account in Galaxy from being an internal to an external account? Ryan ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Development/production instances updates management
We do exactly this. We have a staging instance, and a production instance. Both exist in a single git repo as separate branches. The main different for this is that the staging and production config file point to different port and database instances. We also maintain a staging and production python environment to match. Changes always flow from staging to production and follow the git branch modeling from http://nvie.com/posts/a-successful-git-branching-model/ This has worked EXTREMELY well for us. On Wed, Aug 31, 2016 at 3:00 AM, Mathieu Bahin < mathieu.ba...@biologie.ens.fr> wrote: > Hi all, > > First of all, I'm new to this list and already posted my question on > biostar. Thanks to Hans-Rudolf for his answer but I'm not sure we have > exactly the same constraints here and I send this message to try to get > other answers and see what is the best solution for us. > > I'm trying to setup a good galaxy environment for a biology institute. > To do so, I need to have a development and a production instances that > are clones on the structure side. I'd like to update regularly these > instances (following more or less galaxy main updates) and track them > with git repos. > > I'm pretty sure lot of galaxy admins are trying to do that but I can't > find the answer. > > My idea was to have a local git repo to save the development instance > (not the data). When there is a new update, I git pull it from galaxy > GitHub, compare what changed in the sample files and make the > appropriate changes in the config files corresponding to these samples. > Then I would git push towards the production instance. To do so, I need > to have a proper .gitignore file (listing especially the data files). I > saw that there is a .gitignore in the galaxy GitHub repo. It's probably > relevant when I want to pull the updates but I'm not sure it is > regarding the transfers between the development and production instances > (for example, the config files have to be tracked I guess). > > Cheers, > Mathieu > > -- > > --- > | Mathieu Bahin > | IE CNRS > | > | Institut de Biologie de l'Ecole Normale Supérieure (IBENS) > | Biocomp team > | 46 rue d'Ulm > | 75230 PARIS CEDEX 05 > | 01.44.32.23.56 > > --- > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] provide a field to upload a file as part of tool input
I figured out the optional part (RTFM to myself) On Fri, Aug 5, 2016 at 6:54 PM, Ryan G wrote: > Hi all - I have a custom tool that can optionally take a file as input. > > Right now, users have to upload the file into their history, then select > the file when running the tool. > > Is there a way to let the user select a file local on their computer as > input to the tool, then when run, the file is uploaded? > > And (second question), how can I make this field optional, such that the > user does not need to provide a file at all when running the tool? > > Right now, my input field is: > > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] provide a field to upload a file as part of tool input
Hi all - I have a custom tool that can optionally take a file as input. Right now, users have to upload the file into their history, then select the file when running the tool. Is there a way to let the user select a file local on their computer as input to the tool, then when run, the file is uploaded? And (second question), how can I make this field optional, such that the user does not need to provide a file at all when running the tool? Right now, my input field is: ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Removing job in error state
Thanks. That fixed it. On Thu, Aug 4, 2016 at 3:19 AM, Hans-Rudolf Hotz wrote: > Hi Ryan > > If the "Stop Jobs" option on the Admin page does not work, you can go for > the direct way by manually interacting with the PostgreSQL database: > > Change the state to "error" in the 'job' table, eg: > > update job set state='error' where id=12772; > > > As always, be very careful when you directly access the PostgreSQL > database! Make sure your database is properly backed up. And you should > only consider this as the very last option. > > > Hans-Rudolf > > > On 08/04/2016 06:02 AM, Ryan G wrote: > >> Hi - In the Manage Jobs admin job, I have a job from a user that never >> ran successfully. It shows: >> Job ID UserLast Update ToolState Inputs Command Line >> Job Runner >> PID/Cluster ID >> 12772 u...@company.com <mailto:u...@company.com> 654 >> hours ago >> cshl_fastx_collapsernew 13653 error NoneNoneNone >> >> >> How do I remove this job? I can't find a way to delete it. >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >>https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >>http://galaxyproject.org/search/mailinglists/ >> >> ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Removing job in error state
Hi - In the Manage Jobs admin job, I have a job from a user that never ran successfully. It shows: Job ID User Last Update Tool State Inputs Command Line Job Runner PID/Cluster ID 12772 u...@company.com 654 hours ago cshl_fastx_collapser new 13653 error None None None How do I remove this job? I can't find a way to delete it. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] possible bug found - unable to log out of impersonated user when external authentication enabled
Hi Dannon - We are using 15.10. We have an Apache Proxy server sitting in front of Galaxy and handling the SSO. There is no non-standard routing in place. Yes, when I navigate to the /user/logout url, I get the "Access to Galaxy user controls is disabled" message. On Thu, Jul 28, 2016 at 12:16 AM, Dannon Baker wrote: > I did a bit of digging here, and it looks to me like /user/logout should > be whitelisted in the middleware, and shouldn't present that "Access to > Galaxy user controls is disabled". > > I might need a little more information. What revision of Galaxy are you > running? Are you serving Galaxy at a subdomain or is any other nonstandard > routing in place? As an admin user, if you just directly navigate > to http:///user/logout, you get the same > path-blocked error message? > > On Wed, Jul 27, 2016 at 1:15 PM Ryan G > wrote: > >> Thanks. Clearing out the browser history resolved it but there should be >> a better way... >> >> On Wed, Jul 27, 2016 at 12:48 PM, Dannon Baker >> wrote: >> >>> Hey, thanks for this. I've made an issue ( >>> https://github.com/galaxyproject/galaxy/issues/2671) and will check it >>> out today. >>> >>> On Wed, Jul 27, 2016 at 12:44 PM Ryan G >>> wrote: >>> >>>> Hi all - We are using a SSO system so that user's authenticate >>>> externally from Galaxy. >>>> >>>> when I impersonate a user then try to log out as that user, I'm unable >>>> to. I get the page " >>>> Access to Galaxy user controls is disabled >>>> >>>> User controls are disabled when Galaxy is configured for external >>>> authentication." >>>> >>>> >>>> If I close the browser down, and restart, I get my SSO log in page, but >>>> when I get to Galaxy, I'm still impersonating the user. >>>> >>>> >>>> ___ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> https://lists.galaxyproject.org/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>> >>> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] possible bug found - unable to log out of impersonated user when external authentication enabled
Thanks. Clearing out the browser history resolved it but there should be a better way... On Wed, Jul 27, 2016 at 12:48 PM, Dannon Baker wrote: > Hey, thanks for this. I've made an issue ( > https://github.com/galaxyproject/galaxy/issues/2671) and will check it > out today. > > On Wed, Jul 27, 2016 at 12:44 PM Ryan G > wrote: > >> Hi all - We are using a SSO system so that user's authenticate externally >> from Galaxy. >> >> when I impersonate a user then try to log out as that user, I'm unable >> to. I get the page " >> Access to Galaxy user controls is disabled >> >> User controls are disabled when Galaxy is configured for external >> authentication." >> >> >> If I close the browser down, and restart, I get my SSO log in page, but >> when I get to Galaxy, I'm still impersonating the user. >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] possible bug found - unable to log out of impersonated user when external authentication enabled
Hi all - We are using a SSO system so that user's authenticate externally from Galaxy. when I impersonate a user then try to log out as that user, I'm unable to. I get the page " Access to Galaxy user controls is disabled User controls are disabled when Galaxy is configured for external authentication." If I close the browser down, and restart, I get my SSO log in page, but when I get to Galaxy, I'm still impersonating the user. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] showing progress on running tasks
Hi Martin - I was actually thinking to let the tool itself tell Galaxy about the progress instead of Galaxy estimating that. If instance, if the tool know it has 5 stages, it can report back to Galaxy 20,40,60,80,and 100 % complete. I know this is complex but could be a nice feature. Please excuse any typos -- Sent from my iPhone > On Jul 8, 2016, at 10:47 AM, Martin Čech wrote: > > Hi Ryan, > > This is a fairly complex problem because the length of the run depends most > often on input size, job algorithms, and computational capacity all of which > are quite difficult to estimate. > We have discussed it before and one of the ways to approach this is to gather > statistics from as many jobs as possible and then provide the user with some > estimates based on this data on similar jobs to theirs. > > For the way to gather the data please see > https://github.com/galaxyproject/galaxy/pull/2455 from Eric Rasche. With the > data (or at least data format) we can start working on an algorithm that > would make a guess on a new job length. > > However, there are many other approaches to this problem. > > Thanks, > > Martin > >> On Fri, Jul 8, 2016 at 10:34 AM Ryan G wrote: >> Hi all - I know this isn't currently a feature, but wanted to find out about >> what it would take to implement >> >> We developed some custom tools that are long runningmultiple hours. The >> tools run through various steps of an analysis. >> >> Is there a way to display progress of a task in the history? Possibly as a >> small progress bar? Or provide some feedback via an html page in the main >> frame? >> >> Ryan >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] showing progress on running tasks
Hi all - I know this isn't currently a feature, but wanted to find out about what it would take to implement We developed some custom tools that are long runningmultiple hours. The tools run through various steps of an analysis. Is there a way to display progress of a task in the history? Possibly as a small progress bar? Or provide some feedback via an html page in the main frame? Ryan ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tabular file displayed without tabs
That fixes it. Thanks! On Tue, Jun 14, 2016 at 10:33 AM, Dannon Baker wrote: > Ok, so it's definitely the column limit that's causing the unexpected > style-less display. This currently isn't configurable per-galaxy (the plan > was to add more appropriate displays for many-columned files), but here's a > quick gist to show you how you might tweak this locally: > > https://gist.github.com/dannon/f67cccd16f9e8c8776a0032b11d1c5c7 > > This would be really easy to turn into an app configuration setting in > galaxy.ini if it seems like something folks would want though I opted not > to do so originally to avoid configuration bloat for what seemed like a > very niche case. > > On Tue, Jun 14, 2016 at 10:23 AM Ryan G > wrote: > >> No, it happens to all output from this particular tool. >> >> I do see a javascript warning in the console, 'The character encoding of >> a framed document was not declared. The document may appear different if >> view without the document framing it.' >> >> The file does have 64 columns in it. Is there a way to change Galaxy's >> default from 50 to something more? >> >> >> >> On Tue, May 31, 2016 at 8:17 AM, Carl Eberhard >> wrote: >> >>> Strange. Alright, a few questions then: >>> >>> * Is this the only file that this happens to? Do other outputs from this >>> tool produce the same sort of error? >>> * Do you see any javascript errors in the console when attempting the >>> viewing? (how to here: http://webmasters.stackexchange.com/a/77337) >>> >>> On Fri, May 27, 2016 at 12:42 PM, Ryan G >>> wrote: >>> >>>> The format is listed as tabular when I view details. >>>> >>>> In fact, in the preview window in the History Pane, it recognizes there >>>> are columns and that the data is in fact tabular, but when displaying, this >>>> isn't the case. >>>> >>>> >>>> >>>> On Tue, May 24, 2016 at 4:20 PM, Carl Eberhard >>> > wrote: >>>> >>>>> Ok - if it's not zebra striped and it's word wrapping, then it's >>>>> somehow not displaying as tabular - you're correct. >>>>> >>>>> If you click on the 'View details' button of that dataset (the 'i' >>>>> with the circle around it shown when the dataset is expanded in the right >>>>> hand side of the 'Analyze Data' page), what does it list the 'Format' as? >>>>> 'tabular'? (This is also listed as 'Format' in the expanded view itself). >>>>> >>>>> On Mon, May 23, 2016 at 5:33 PM, Ryan G >>>>> wrote: >>>>> >>>>>> Odd because I have another tabular file that is displayed with every >>>>>> other line highlighted and there is not word-wrapping on the file. >>>>>> However >>>>>> the file that has the type tabular and displayed as text is word-wrapped >>>>>> with no lines highlighted. I suspect its not actually recognized as >>>>>> tabular or is being overridden where. >>>>>> >>>>>> >>>>>> On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard < >>>>>> carlfeberh...@gmail.com> wrote: >>>>>> >>>>>>> Hi, Ryan >>>>>>> >>>>>>> Galaxy displays tabular data in the browser using a tag. It >>>>>>> *sounds like* the behavior you see (columns losing space between one >>>>>>> another when narrowing the window and getting more space as you expand >>>>>>> the >>>>>>> window) would reflect that. >>>>>>> >>>>>>> Carl >>>>>>> >>>>>>> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G >>>>>> > wrote: >>>>>>> >>>>>>>> The file is an output from a tool and in the tool's xml, its format >>>>>>>> is tabular. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning < >>>>>>>> bjoern.gruen...@gmail.com> wrote: >>>>>>>> >>>>>>>>> Hi Ryan, >>>>>>>>> >>>>>>>>> is it recognised as 'tabular
Re: [galaxy-dev] tabular file displayed without tabs
No, it happens to all output from this particular tool. I do see a javascript warning in the console, 'The character encoding of a framed document was not declared. The document may appear different if view without the document framing it.' The file does have 64 columns in it. Is there a way to change Galaxy's default from 50 to something more? On Tue, May 31, 2016 at 8:17 AM, Carl Eberhard wrote: > Strange. Alright, a few questions then: > > * Is this the only file that this happens to? Do other outputs from this > tool produce the same sort of error? > * Do you see any javascript errors in the console when attempting the > viewing? (how to here: http://webmasters.stackexchange.com/a/77337) > > On Fri, May 27, 2016 at 12:42 PM, Ryan G > wrote: > >> The format is listed as tabular when I view details. >> >> In fact, in the preview window in the History Pane, it recognizes there >> are columns and that the data is in fact tabular, but when displaying, this >> isn't the case. >> >> >> >> On Tue, May 24, 2016 at 4:20 PM, Carl Eberhard >> wrote: >> >>> Ok - if it's not zebra striped and it's word wrapping, then it's somehow >>> not displaying as tabular - you're correct. >>> >>> If you click on the 'View details' button of that dataset (the 'i' with >>> the circle around it shown when the dataset is expanded in the right hand >>> side of the 'Analyze Data' page), what does it list the 'Format' as? >>> 'tabular'? (This is also listed as 'Format' in the expanded view itself). >>> >>> On Mon, May 23, 2016 at 5:33 PM, Ryan G >>> wrote: >>> >>>> Odd because I have another tabular file that is displayed with every >>>> other line highlighted and there is not word-wrapping on the file. However >>>> the file that has the type tabular and displayed as text is word-wrapped >>>> with no lines highlighted. I suspect its not actually recognized as >>>> tabular or is being overridden where. >>>> >>>> >>>> On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard < >>>> carlfeberh...@gmail.com> wrote: >>>> >>>>> Hi, Ryan >>>>> >>>>> Galaxy displays tabular data in the browser using a tag. It >>>>> *sounds like* the behavior you see (columns losing space between one >>>>> another when narrowing the window and getting more space as you expand the >>>>> window) would reflect that. >>>>> >>>>> Carl >>>>> >>>>> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G >>>>> wrote: >>>>> >>>>>> The file is an output from a tool and in the tool's xml, its format >>>>>> is tabular. >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning < >>>>>> bjoern.gruen...@gmail.com> wrote: >>>>>> >>>>>>> Hi Ryan, >>>>>>> >>>>>>> is it recognised as 'tabular'? >>>>>>> >>>>>>> Ciao, >>>>>>> Bjoern >>>>>>> >>>>>>> Am 27.10.2015 um 04:42 schrieb Ryan G: >>>>>>> > Hi - I have a tools that generates a tab-delimited text file as >>>>>>> output. >>>>>>> > when I click the eye icon to view the data, all the fields are >>>>>>> compressed >>>>>>> > as if there were no tabs. If I expand the history view, the >>>>>>> little preview >>>>>>> > window shows the contents as tabbed. I've verified that the >>>>>>> spaces are >>>>>>> > indeed '\t' tab characters. Why would Galaxy not display this >>>>>>> file as a >>>>>>> > tab-delimited file? >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > ___ >>>>>>> > Please keep all replies on the list by using "reply all" >>>>>>> > in your mail client. To manage your subscriptions to this >>>>>>> > and other Galaxy lists, please use the interface at: >>>>>>> > https://lists.galaxyproject.org/ >>>>>>> > >>>>>>> > To search Galaxy mailing lists use the unified search at: >>>>>>> > http://galaxyproject.org/search/mailinglists/ >>>>>>> > >>>>>>> >>>>>> >>>>>> >>>>>> ___ >>>>>> Please keep all replies on the list by using "reply all" >>>>>> in your mail client. To manage your subscriptions to this >>>>>> and other Galaxy lists, please use the interface at: >>>>>> https://lists.galaxyproject.org/ >>>>>> >>>>>> To search Galaxy mailing lists use the unified search at: >>>>>> http://galaxyproject.org/search/mailinglists/ >>>>>> >>>>> >>>>> >>>> >>> >> > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Bug Found: 2 tabs in browser open to different histories confuses tools
Hi all - I think I found a bug. I have two histories open in two separate tabs in Chrome. When I try to run a tool and select an item from my history, the wrong history items are displayed. Ryan ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tabular file displayed without tabs
The format is listed as tabular when I view details. In fact, in the preview window in the History Pane, it recognizes there are columns and that the data is in fact tabular, but when displaying, this isn't the case. On Tue, May 24, 2016 at 4:20 PM, Carl Eberhard wrote: > Ok - if it's not zebra striped and it's word wrapping, then it's somehow > not displaying as tabular - you're correct. > > If you click on the 'View details' button of that dataset (the 'i' with > the circle around it shown when the dataset is expanded in the right hand > side of the 'Analyze Data' page), what does it list the 'Format' as? > 'tabular'? (This is also listed as 'Format' in the expanded view itself). > > On Mon, May 23, 2016 at 5:33 PM, Ryan G > wrote: > >> Odd because I have another tabular file that is displayed with every >> other line highlighted and there is not word-wrapping on the file. However >> the file that has the type tabular and displayed as text is word-wrapped >> with no lines highlighted. I suspect its not actually recognized as >> tabular or is being overridden where. >> >> >> On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard >> wrote: >> >>> Hi, Ryan >>> >>> Galaxy displays tabular data in the browser using a tag. It >>> *sounds like* the behavior you see (columns losing space between one >>> another when narrowing the window and getting more space as you expand the >>> window) would reflect that. >>> >>> Carl >>> >>> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G >>> wrote: >>> >>>> The file is an output from a tool and in the tool's xml, its format is >>>> tabular. >>>> >>>> >>>> >>>> On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning < >>>> bjoern.gruen...@gmail.com> wrote: >>>> >>>>> Hi Ryan, >>>>> >>>>> is it recognised as 'tabular'? >>>>> >>>>> Ciao, >>>>> Bjoern >>>>> >>>>> Am 27.10.2015 um 04:42 schrieb Ryan G: >>>>> > Hi - I have a tools that generates a tab-delimited text file as >>>>> output. >>>>> > when I click the eye icon to view the data, all the fields are >>>>> compressed >>>>> > as if there were no tabs. If I expand the history view, the little >>>>> preview >>>>> > window shows the contents as tabbed. I've verified that the spaces >>>>> are >>>>> > indeed '\t' tab characters. Why would Galaxy not display this file >>>>> as a >>>>> > tab-delimited file? >>>>> > >>>>> > >>>>> > >>>>> > ___ >>>>> > Please keep all replies on the list by using "reply all" >>>>> > in your mail client. To manage your subscriptions to this >>>>> > and other Galaxy lists, please use the interface at: >>>>> > https://lists.galaxyproject.org/ >>>>> > >>>>> > To search Galaxy mailing lists use the unified search at: >>>>> > http://galaxyproject.org/search/mailinglists/ >>>>> > >>>>> >>>> >>>> >>>> ___ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> https://lists.galaxyproject.org/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>>> >>> >>> >> > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tabular file displayed without tabs
Odd because I have another tabular file that is displayed with every other line highlighted and there is not word-wrapping on the file. However the file that has the type tabular and displayed as text is word-wrapped with no lines highlighted. I suspect its not actually recognized as tabular or is being overridden where. On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard wrote: > Hi, Ryan > > Galaxy displays tabular data in the browser using a tag. It > *sounds like* the behavior you see (columns losing space between one > another when narrowing the window and getting more space as you expand the > window) would reflect that. > > Carl > > On Wed, Oct 28, 2015 at 1:23 PM, Ryan G > wrote: > >> The file is an output from a tool and in the tool's xml, its format is >> tabular. >> >> >> >> On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning > > wrote: >> >>> Hi Ryan, >>> >>> is it recognised as 'tabular'? >>> >>> Ciao, >>> Bjoern >>> >>> Am 27.10.2015 um 04:42 schrieb Ryan G: >>> > Hi - I have a tools that generates a tab-delimited text file as output. >>> > when I click the eye icon to view the data, all the fields are >>> compressed >>> > as if there were no tabs. If I expand the history view, the little >>> preview >>> > window shows the contents as tabbed. I've verified that the spaces are >>> > indeed '\t' tab characters. Why would Galaxy not display this file as >>> a >>> > tab-delimited file? >>> > >>> > >>> > >>> > ___ >>> > Please keep all replies on the list by using "reply all" >>> > in your mail client. To manage your subscriptions to this >>> > and other Galaxy lists, please use the interface at: >>> > https://lists.galaxyproject.org/ >>> > >>> > To search Galaxy mailing lists use the unified search at: >>> > http://galaxyproject.org/search/mailinglists/ >>> > >>> >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] output datasets
Yes that's exactly what I ended up doing.
Please excuse any typos -- Sent from my iPhone
> On Apr 26, 2016, at 4:01 PM, Marius van den Beek
> wrote:
>
> Hi Ryan,
>
> I think you could create two regular outputs, and move the files to those
> outputs, i.e:
>
> ```
>
>
>
>
>
>
>
>
>
>
> ```
>
> I understand that you would also like to keep the $sraid id in the history,
> right?
> For that you should be able use `label="${sraid}.txt` on your outputs.
>
> Cheers,
> Marius
>
>> On 26 April 2016 at 20:46, Ryan G wrote:
>> I'm playing around with creating a Galaxy wrapper for custom tool I've
>> created. My tool takes a single parameter, and SRA ID. In command block, I
>> have something like this:
>>
>>
>> ${GALAXY_ROOT_DIR}/tools/mycustomtools/doSomething.pl --sra $sraid
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Galaxy doesn't like thr $sraid in the output. I see from the docs I need to
>> use discover_datasets. It would be nice to use a parameter such as what I
>> have to name output file as my script names output files use an input
>> parameter as the base.
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>
___
Please keep all replies on the list by using "reply all"
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and other Galaxy lists, please use the interface at:
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[galaxy-dev] output datasets
I'm playing around with creating a Galaxy wrapper for custom tool I've
created. My tool takes a single parameter, and SRA ID. In command block,
I have something like this:
${GALAXY_ROOT_DIR}/tools/mycustomtools/doSomething.pl --sra $sraid
Galaxy doesn't like thr $sraid in the output. I see from the docs I need
to use discover_datasets. It would be nice to use a parameter such as
what I have to name output file as my script names output files use an
input parameter as the base.
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Python 2.7 vs 2.6 for galaxy after 16.01
We Iocally compile 2.7.8 and keep it in a distinct location that our paths references. This is very easy and has worked well for us. Please excuse any typos -- Sent from my iPhone > On Mar 21, 2016, at 5:32 PM, Peter Cock wrote: > > Hi D. K., > > We're currently trying a locally compiled Python 2.7 (from source) > under the shared Galaxy mount for use with a CentOS 6 cluster > and Galaxy server. > > This seems to be working once we got the $PATH working for > cluster jobs (initially they would try to set the Galaxy metadata > using the system Python 2.6, which would fail). > > I don't know if this is any easier than using the CenOS Software > Collections as suggested by Nicola, especially when it comes to > updating the OS. > > Peter > >> On Mon, Mar 21, 2016 at 5:59 PM, Nicola Soranzo wrote: >> Hi Daniel, >> I've been using python27 from CentOS Software Collections for quite some >> time. It's a bit annoying because you have to remember to load it, but it is >> surely doable. >> >> Cheers, >> Nicola >> >> >> On 21/03/16 17:46, D K wrote: >> >> Hi Galaxy Devs, >> >> This may be premature but I read that for Galaxy after 16.01 that the plan >> is for python 2.6 to no longer be supported. I'm currently running CentOS >> 6.6 which uses python 2.6. In order to be able to use newer versions of >> Galaxy is my only option to upgrade to a newer version of CentOS? Is it >> possible to use Conda, RedHat Software Collections or some other similar >> method instead of doing this upgrade? >> >> Thanks! >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Cloudman & AWS IAM_PROFILE support?
We actually have galaxy running within a VPC now. The problem we're running into is that when ec2 instances get created they don't have an I_am profile attached to them so they can't get access to S3 resources. This should just be a parameter past to AWS when the instances get created to attach the Iam profile. I just need to know where the code for creating ec2 instances is and I can test it out. Please excuse any typos -- Sent from my iPhone > On Mar 15, 2016, at 10:46 PM, Chris Dagdigian wrote: > > > Hi Ryan, > > I've never been able to get cloudman to function within a private VPC so if > this is your architecture as well and you manage to make progress I'd be > interested in learning your methods. Thanks! > > Regards, > Chris > > > Enis Afgan wrote: >> Hi Ryan, >> I'm not sure I really understand your question but CloudMan can run under an >> IAM account - it is just necessary to give the IAM user permissions to >> create EC2 and S3 resources. Let us know if that's not what you had in mind >> or if you have any more questions. >> >> Cheers, >> Enis > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Cloudman & AWS IAM_PROFILE support?
Hi - Does Cloudman support IAM_PROFILES? We run our instances within a VPC and assign an IAM_PROFILE to the ec2 instances so that they have access to resouces. Does Cloudman have this support? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy 15.10 Jobs not running
Hi Nate - Thanks. Our galaxy.ini shows: job_config_file = config/job_conf.xml Our job_conf.xml is (which is the same as job_conf.xml.sample_basic) : Hmmm, ok weird. We just restart Galaxy for the 5th or 6th time to get a clean log file to send and it works now. Hmmm. I will consider this issue closed. Is there any documention that talks about how the job runner and manager, all work together? I'd like to add some debugging statements in the code so there is more info in the log file. On Wed, Mar 2, 2016 at 12:00 PM, Nate Coraor wrote: > On Tue, Mar 1, 2016 at 1:19 PM, Ryan G > wrote: > >> Hi all - We recently merged in Galaxy 15.10 changes into our staging >> instance and have noticed jobs are no longer dispatched. There is no >> obvious problem in the log file. >> >> I see in github, commits have recently been made to revert something, but >> I'm not clear what. >> >> Is there something going on with the job runner? Better yet, how can I >> track down what my issue is? >> > > Hi Ryan, > > There aren't any current issues with job running that I'm aware of. > Typically the first thing to check is your job_conf.xml and make sure that > handlers defined are the same as handlers (with matching server names) that > you are starting). The log for your handlers should show them loading the > job_conf.xml and setting up job plugins if they are identified as handlers > in the config. > > --nate > > >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy 15.10 Jobs not running
Hi all - We recently merged in Galaxy 15.10 changes into our staging instance and have noticed jobs are no longer dispatched. There is no obvious problem in the log file. I see in github, commits have recently been made to revert something, but I'm not clear what. Is there something going on with the job runner? Better yet, how can I track down what my issue is? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Custom tool with multiple inputs for different datasets. How to preferrentially select
Next question - My custom tool take as input mulitple datasets from different tools and collates all the information. For instance, 1 input as tabular input, sampleManifest, another input is also tabular, expressionData. When the tool is display, both entries default to the most recent tabular dataset in the history. Is there a way to have Galaxy try to guess which dataset to default to as input instead of always choosing the latest input for all the fields? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Restricting tool input to 1 dataset instead of multiple
Hi all - I'm creating a tool in Galaxy that takes as input several datasets for different variables. For each variable, I want to restrict the input to a single dataset. The docs, https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax, indicate type="data" needs to be set for a dataset from the current history to be available for input. When I do this, Galaxy displays the icon for Single Dataset, Mulitple Datasets, and Dataset collection. I only want to give the option for Single Dataset. I tried include multiple="false", but that doesn't seem to have any effect. Is there a way to accomplish this? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] It would be nice to know that labels can only be lowercase in format tags
This is why I think Galaxy unit tests really need to be up to date and working thoroughly. Something like this could have been easily caught. On Thu, Feb 18, 2016 at 7:31 PM, wrote: > Good evening, > Having wasted multiple hours it would be helpful to see in the > documentation that only LOWERCASE is allowed for defining unique file > extensions to link specific files output by one tool as a particular input > to another tool. > type="galaxy.datatypes.data:Text" sub display_in_upload="True"/> > outgoing tool's xml > label=""/> > Accepting tool's xml > label="" /> > It would be great to know up-front the format can only be LOWER CASE -- no > error message, no ignoring upper or lower and treating the same. Just > failure when trying to run it. > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Login reguried causing nested main page loading
I've seen this as well. I find that restarting galaxy fixes the problem but I'd love to know the underlying cause. Please excuse any typos -- Sent from my iPhone > On Jan 11, 2016, at 5:08 AM, Christian Brenninkmeijer > wrote: > > Hi All, > > I tried to turn on login required in config.ini > > But now if you are not logged in it loads the main page where normally the > welcome.html would go. > Which then recursively loads other main pages. > > Which file am I missing? > > Thanks > Christian > University of Manchester > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Cloudman vs StarCluster
Hi all - Our organization requires us to use a specific AMI (with a specific flavor of linux) that isn't supported by Cloudman. Its taking us a bit of time to get this combination working. Its taken more than 3 weeks and we still don't have Galaxy / Cloudman running. I could probably do the same thing with StarCluster and be up and running within a day. I'm very comfortable with using StarCluster and am wondering if there is any benefit to using Cloudman over StarCluster for node management with Galaxy. Thoughts? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] feature request
Thanks. On Mon, Nov 9, 2015 at 4:40 PM, Martin Čech wrote: > Created it for you here: > https://github.com/galaxyproject/galaxy/issues/1045 > > > On Mon, Nov 9, 2015 at 4:39 PM Ryan G wrote: > >> Yes, I'll do it there. >> >> On Mon, Nov 9, 2015 at 4:38 PM, Björn Grüning >> wrote: >> >>> Hi Ryan, >>> >>> can you create a github issue with this suggestion :) >>> >>> Thanks, >>> Bjoern >>> >>> Am 09.11.2015 um 22:37 schrieb Ryan G: >>> > I'd put this into Trello, but Trello is blocked from my place of >>> business... >>> > >>> > I have a data library with over 200 files in it. Half of them are >>> > "clipped" and the other half are not. I'd like to be able to search >>> and >>> > display a subset of files in the data library. This will make >>> selecting >>> > the files I want to import into my history much easier. >>> > >>> > >>> > >>> > ___ >>> > Please keep all replies on the list by using "reply all" >>> > in your mail client. To manage your subscriptions to this >>> > and other Galaxy lists, please use the interface at: >>> > https://lists.galaxyproject.org/ >>> > >>> > To search Galaxy mailing lists use the unified search at: >>> > http://galaxyproject.org/search/mailinglists/ >>> > >>> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] feature request
Yes, I'll do it there. On Mon, Nov 9, 2015 at 4:38 PM, Björn Grüning wrote: > Hi Ryan, > > can you create a github issue with this suggestion :) > > Thanks, > Bjoern > > Am 09.11.2015 um 22:37 schrieb Ryan G: > > I'd put this into Trello, but Trello is blocked from my place of > business... > > > > I have a data library with over 200 files in it. Half of them are > > "clipped" and the other half are not. I'd like to be able to search and > > display a subset of files in the data library. This will make selecting > > the files I want to import into my history much easier. > > > > > > > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] feature request
I'd put this into Trello, but Trello is blocked from my place of business... I have a data library with over 200 files in it. Half of them are "clipped" and the other half are not. I'd like to be able to search and display a subset of files in the data library. This will make selecting the files I want to import into my history much easier. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tabular file displayed without tabs
The file is an output from a tool and in the tool's xml, its format is tabular. On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning wrote: > Hi Ryan, > > is it recognised as 'tabular'? > > Ciao, > Bjoern > > Am 27.10.2015 um 04:42 schrieb Ryan G: > > Hi - I have a tools that generates a tab-delimited text file as output. > > when I click the eye icon to view the data, all the fields are compressed > > as if there were no tabs. If I expand the history view, the little > preview > > window shows the contents as tabbed. I've verified that the spaces are > > indeed '\t' tab characters. Why would Galaxy not display this file as a > > tab-delimited file? > > > > > > > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] tabular file displayed without tabs
Hi - I have a tools that generates a tab-delimited text file as output. when I click the eye icon to view the data, all the fields are compressed as if there were no tabs. If I expand the history view, the little preview window shows the contents as tabbed. I've verified that the spaces are indeed '\t' tab characters. Why would Galaxy not display this file as a tab-delimited file? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] external authentication - empty REMOTE_USER
Here is the pull request: https://github.com/galaxyproject/galaxy/pull/823
You can see what file was edited
On Wed, Oct 21, 2015 at 8:40 AM, Floreline TOUCHARD <
floreline.touch...@gmail.com> wrote:
> Thank you ! Can you tell me which files are to update or download ?
> I installed my application on a server that was not open to the outside.
> Currently I do not support different versions or updates of my application
> with git.
> I can download the files to edit and transfer them to the server but not
> to update the entire application at the moment.
>
> F. T
> Le 21 oct. 2015 12:11 PM, "Floreline TOUCHARD" <
> floreline.touch...@gmail.com> a écrit :
>
>> Hi,
>>
>> I've got an issue with my external authentication configuration. I use
>> Apache and the mod_perl
>>
>> modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with
>> NIS accounts.
>>
>> I have the authentication form when I try to access galaxy web page.
>> But after a successful authentication it seems that the REMOTE_USER
>> variable is not passed to my galaxy instance. I'm connected under "@
>> example.org" regardless of the authentication account. That's why I
>> think the REMOTE_USER passed to Galaxy is not 'null' but empty.
>>
>> I tested the value of the variable with the following php script:
>>
>> > foreach($_SERVER as $key_name => $key_value) {
>> print $key_name . " = " . $key_value . "";
>>
>> }
>>
>> ?>
>>
>> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
>>
>> I don't understand where my problem lies.
>>
>>
>>
>> Here is my galaxy.conf file :
>>
>> Listen 2208
>>
>>
>>
>>
>> RewriteEngine on
>> DocumentRoot "/path/to/static"
>>
>>
>>
>>
>> Options +Indexes FollowSymLinks MultiViews
>> AllowOverride None
>> Order allow,deny
>> Allow from all
>>
>>
>> AuthType Basic
>> AuthName "Authentifiez vous"
>> PerlAuthenHandler Apache2::AuthenNIS
>> PerlAuthzHandler Apache2::AuthzNIS
>> PerlSetVar AllowAlternateAuth no
>> require valid-user
>>
>>
>>
>>
>>
>> RewriteEngine on
>> RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
>> RequestHeader set REMOTE_USER %{RU}e
>>
>>
>>
>>RewriteRule ^/galaxy$ /galaxy/ [R]
>>RewriteRule ^/static/style/(.*)
>> /path/to/static/june_2007_style/blue/$1 [L]
>>RewriteRule ^/static/scripts/(.*)
>> /softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1
>>
>> [L]
>>RewriteRule ^/static/(.*) /path/to/static/$1 [L]
>>RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
>>RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
>>RewriteRule ^(.*) http://localhost:2209$1 [P]
>>
>>
>>
>>
>>
>> Thanks in advance !
>>
>> F.T
>>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> https://lists.galaxyproject.org/
>
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>
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Re: [galaxy-dev] external authentication - empty REMOTE_USER
I just recently submitted a patch that will display all the environment
variables being passed to Galaxy in pastor.log. That should help you determine
if the variables are set and to what.
Please excuse any typos -- Sent from my iPhone
> On Oct 21, 2015, at 6:11 AM, Floreline TOUCHARD
> wrote:
>
> Hi,
>
> I've got an issue with my external authentication configuration. I use Apache
> and the mod_perl
>
> modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with NIS
> accounts.
>
> I have the authentication form when I try to access galaxy web page.
> But after a successful authentication it seems that the REMOTE_USER variable
> is not passed to my galaxy instance. I'm connected under "@example.org"
> regardless of the authentication account. That's why I think the REMOTE_USER
> passed to Galaxy is not 'null' but empty.
>
> I tested the value of the variable with the following php script:
>
> foreach($_SERVER as $key_name => $key_value) {
> print $key_name . " = " . $key_value . "";
>
> }
>
> ?>
>
> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
>
> I don't understand where my problem lies.
>
>
>
> Here is my galaxy.conf file :
>
> Listen 2208
>
>
>
>
> RewriteEngine on
> DocumentRoot "/path/to/static"
>
>
>
>
> Options +Indexes FollowSymLinks MultiViews
> AllowOverride None
> Order allow,deny
> Allow from all
>
>
> AuthType Basic
> AuthName "Authentifiez vous"
> PerlAuthenHandler Apache2::AuthenNIS
> PerlAuthzHandler Apache2::AuthzNIS
> PerlSetVar AllowAlternateAuth no
> require valid-user
>
>
>
>
>
> RewriteEngine on
> RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
> RequestHeader set REMOTE_USER %{RU}e
>
>
>
>RewriteRule ^/galaxy$ /galaxy/ [R]
>RewriteRule ^/static/style/(.*) /path/to/static/june_2007_style/blue/$1 [L]
>RewriteRule ^/static/scripts/(.*)
> /softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1
>
> [L]
>RewriteRule ^/static/(.*) /path/to/static/$1 [L]
>RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
>RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
>RewriteRule ^(.*) http://localhost:2209$1 [P]
>
>
>
>
>
> Thanks in advance !
>
> F.T
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
___
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Re: [galaxy-dev] External User Authenticaion
Thanks. I'll try that. On Tue, Oct 13, 2015 at 12:52 PM, Eric Rasche wrote: > Howdy Ryan, > > On 10/13/2015 11:44 AM, Ryan G wrote: > > Sorry, maybe I'm not being clear. > > > > Galaxy is listening on http://galaxy.mycompany.com:8080 > > > > Users access Galaxy via http://mycompay.com/galaxy > > Ah! This is much more clear, thanks :) > > If you're running under remote_user, you should NOT make it available > outside of the apache proxy. Even with the remote_user_secret variable > that was added, it's still an unnecessary security risk. > > > If users go to http://galaxy.mycompany.com:8080, they get the External > > Authentication message. From here I want them to be redirected to > > http://mycompay.com/galaxy which is where they will be authenticated. > > I'm guessing you migrated at some point from the raw port to the /galaxy > address and your users are moving slowly to the new URL. > > Here is my suggestion: > > - have galaxy listen on 127.0.0.1:8081 so only apache on the same > machine can access it. > - add an apache virtualhost listening on 0.0.0.0:8080 that automatically > redirects any requests to that page to http://mycompany.com/galaxy/ to > help migrate users. > > That should fix your problem without requiring modification to your > codebase for this one scenario. > > > > > Users never see http://galaxy.mycompany.com:8080they will always see > > http://mycompay.com/galaxy > > > > > > > > > > > On Tue, Oct 13, 2015 at 12:36 PM, Eric Rasche > <mailto:e...@tamu.edu>> wrote: > > > > > > > > On 10/13/2015 11:34 AM, Ryan G wrote: > > > We have Apache set up to authenticate users off our LDAP. If they > > > authenticate correctly, they are then forwarded on through the > proxy. > > > > So, mod_auth_ldap? Or not? You say "forwarded" so I'm thinking you > may > > not mean this. > > > > > > > > What I want is to prevent users from hitting the galaxy URL > directly. > > > If they, do I want to automatically redirect them to the proxy. > > > > Under mod_auth_ldap this should be done for you. > > > > (Worst case scenario you could write some mod_rewrite logic that > checks > > for the remote_user header and returns a 301 if it's missing with the > > location of your login page) > > > > > > > > > > > On Tue, Oct 13, 2015 at 11:10 AM, Eric Rasche <mailto:e...@tamu.edu> > > > <mailto:e...@tamu.edu <mailto:e...@tamu.edu>>> wrote: > > > > > > Hi Ryan, > > > > > > On 10/13/2015 09:50 AM, Ryan G wrote: > > > > Hi all - In regards to external user authentication that I > have working > > > > now (see thread below). When users try to go to the actual > Galaxy page, > > > > they get the message: > > > > > > > > > > > > Access to Galaxy is denied > > > > > > That's expected for External User Auth if you don't have the > REMOTE_USER > > > header set properly. > > > > > > > > > > > Galaxy is configured to authenticate users via an external > method (such > > > > as HTTP authentication in Apache), but no shared secret key > was provided > > > > by the upstream (proxy) server. > > > > > > > > Please contact your local Galaxy administrator. The variable > > > > |remote_user_secret| and |GX_SECRET| header must be set > before you may > > > > access Galaxy. > > > > > > > > > > > > > > > > That's fine and all but I'd like to have them redirected to > the real > > > > login page. Is there a way to do this? I didn't see > anything obvious > > > > and was thinking of adding a parameter to galaxy.ini and > have Galaxy > > > > automatically forward them after 5 seconds or so. > > > > > > What external auth mechanism are you using? > > > > > > > > > > > Ryan > > > > > > > > > > > > On Tue, Oct 13, 2015 at 10:49 AM, Ryan G < > ngsbioinformat...@gmail.com <mailto:ngsbioinformat...@
Re: [galaxy-dev] External User Authenticaion
Sorry, maybe I'm not being clear. Galaxy is listening on http://galaxy.mycompany.com:8080 Users access Galaxy via http://mycompay.com/galaxy If users go to http://galaxy.mycompany.com:8080, they get the External Authentication message. From here I want them to be redirected to http://mycompay.com/galaxy which is where they will be authenticated. Users never see http://galaxy.mycompany.com:8080they will always see http://mycompay.com/galaxy On Tue, Oct 13, 2015 at 12:36 PM, Eric Rasche wrote: > > > On 10/13/2015 11:34 AM, Ryan G wrote: > > We have Apache set up to authenticate users off our LDAP. If they > > authenticate correctly, they are then forwarded on through the proxy. > > So, mod_auth_ldap? Or not? You say "forwarded" so I'm thinking you may > not mean this. > > > > > What I want is to prevent users from hitting the galaxy URL directly. > > If they, do I want to automatically redirect them to the proxy. > > Under mod_auth_ldap this should be done for you. > > (Worst case scenario you could write some mod_rewrite logic that checks > for the remote_user header and returns a 301 if it's missing with the > location of your login page) > > > > > > > On Tue, Oct 13, 2015 at 11:10 AM, Eric Rasche > <mailto:e...@tamu.edu>> wrote: > > > > Hi Ryan, > > > > On 10/13/2015 09:50 AM, Ryan G wrote: > > > Hi all - In regards to external user authentication that I have > working > > > now (see thread below). When users try to go to the actual Galaxy > page, > > > they get the message: > > > > > > > > > Access to Galaxy is denied > > > > That's expected for External User Auth if you don't have the > REMOTE_USER > > header set properly. > > > > > > > > Galaxy is configured to authenticate users via an external method > (such > > > as HTTP authentication in Apache), but no shared secret key was > provided > > > by the upstream (proxy) server. > > > > > > Please contact your local Galaxy administrator. The variable > > > |remote_user_secret| and |GX_SECRET| header must be set before you > may > > > access Galaxy. > > > > > > > > > > > > That's fine and all but I'd like to have them redirected to the > real > > > login page. Is there a way to do this? I didn't see anything > obvious > > > and was thinking of adding a parameter to galaxy.ini and have > Galaxy > > > automatically forward them after 5 seconds or so. > > > > What external auth mechanism are you using? > > > > > > > > Ryan > > > > > > > > > On Tue, Oct 13, 2015 at 10:49 AM, Ryan G < > ngsbioinformat...@gmail.com <mailto:ngsbioinformat...@gmail.com> > > > <mailto:ngsbioinformat...@gmail.com ngsbioinformat...@gmail.com>>> > > wrote: > > > > > > Hi all - In regards to external user authentication that I have > > > working now (see thread below). When users try to go to the > actual > > > Galaxy page, they get the message: > > > > > > > > > On Thu, Oct 1, 2015 at 4:10 PM, Ryan G < > ngsbioinformat...@gmail.com <mailto:ngsbioinformat...@gmail.com> > > > <mailto:ngsbioinformat...@gmail.com ngsbioinformat...@gmail.com>>> > > wrote: > > > > > > I finally got around to this and all is working well. I > > > submitted 2 patches to remoteuser.py to assist in debugging > > > incorrect set ups. > > > > > > Last question - When a user logs out, they get the page > ""Access > > > to Galaxy user controls is disabled". I've set the > > > remote_user_logout_href parameter to a different website, > but > > > they still get the "Access to Galaxy user controls is > disabled". > > > > > > I see it in lib/galaxy/webapps/galaxy/controllers/user.py, > but I > > > think at that point its too late. > > > > > > > > > > > > On Tue, Sep 8, 2015 at 4:05 PM, Ryan G > > > ngsbioinformat...@gmail.com> > > > <mailto:ngsbioinformat...@gmail.com ngsbioinformat...@gmail.com>>> > >
Re: [galaxy-dev] External User Authenticaion
We have Apache set up to authenticate users off our LDAP. If they authenticate correctly, they are then forwarded on through the proxy. What I want is to prevent users from hitting the galaxy URL directly. If they, do I want to automatically redirect them to the proxy. On Tue, Oct 13, 2015 at 11:10 AM, Eric Rasche wrote: > Hi Ryan, > > On 10/13/2015 09:50 AM, Ryan G wrote: > > Hi all - In regards to external user authentication that I have working > > now (see thread below). When users try to go to the actual Galaxy page, > > they get the message: > > > > > > Access to Galaxy is denied > > That's expected for External User Auth if you don't have the REMOTE_USER > header set properly. > > > > > Galaxy is configured to authenticate users via an external method (such > > as HTTP authentication in Apache), but no shared secret key was provided > > by the upstream (proxy) server. > > > > Please contact your local Galaxy administrator. The variable > > |remote_user_secret| and |GX_SECRET| header must be set before you may > > access Galaxy. > > > > > > > > That's fine and all but I'd like to have them redirected to the real > > login page. Is there a way to do this? I didn't see anything obvious > > and was thinking of adding a parameter to galaxy.ini and have Galaxy > > automatically forward them after 5 seconds or so. > > What external auth mechanism are you using? > > > > > Ryan > > > > > > On Tue, Oct 13, 2015 at 10:49 AM, Ryan G > <mailto:ngsbioinformat...@gmail.com>> wrote: > > > > Hi all - In regards to external user authentication that I have > > working now (see thread below). When users try to go to the actual > > Galaxy page, they get the message: > > > > > > On Thu, Oct 1, 2015 at 4:10 PM, Ryan G > <mailto:ngsbioinformat...@gmail.com>> wrote: > > > > I finally got around to this and all is working well. I > > submitted 2 patches to remoteuser.py to assist in debugging > > incorrect set ups. > > > > Last question - When a user logs out, they get the page ""Access > > to Galaxy user controls is disabled". I've set the > > remote_user_logout_href parameter to a different website, but > > they still get the "Access to Galaxy user controls is disabled". > > > > I see it in lib/galaxy/webapps/galaxy/controllers/user.py, but I > > think at that point its too late. > > > > > > > > On Tue, Sep 8, 2015 at 4:05 PM, Ryan G > > > <mailto:ngsbioinformat...@gmail.com>> wrote: > > > > Yes, I have a test server I'm going to check this one. > > thanks for the link, that's perfect...I'll add some > > debugging code in here to see what's going on. > > > > On Tue, Sep 8, 2015 at 1:46 PM, Dannon Baker > > mailto:dannon.ba...@gmail.com>> > wrote: > > > > Do you have a way to verify the "HTTP_MAIL" header is > > actually being passed through your proxy server? > > > > The problem is that Galaxy still doesn't think it's > > receiving the expected headers, so there isn't a good > > way that it can tell you more about what might be going > > on. If you're able to tweak Galaxy (using a test > > server) and add a few logging statements the code, this > > would be good places to check what's going on (print the > > `environ` dictionary associated with that request, along > > with self.remote_user_header to see what Galaxy is > > actually trying to use): > > > > > https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/framework/middleware/remoteuser.py#L49 > > > > -Dannon > > > > On Thu, Sep 3, 2015 at 1:51 PM, Ryan G > > > <mailto:ngsbioinformat...@gmail.com>> wrote: > > > > It turns out our authentication system passes a > > header 'HTTP_MAIL' which contains the users email > > address. In galaxy.ini, I have > > > > use_remote_user = True > > remote_user_header = HTTP_MAIL > > &g
Re: [galaxy-dev] External User Authenticaion
Hi all - In regards to external user authentication that I have working now (see thread below). When users try to go to the actual Galaxy page, they get the message: On Thu, Oct 1, 2015 at 4:10 PM, Ryan G wrote: > I finally got around to this and all is working well. I submitted 2 > patches to remoteuser.py to assist in debugging incorrect set ups. > > Last question - When a user logs out, they get the page ""Access to Galaxy > user controls is disabled". I've set the remote_user_logout_href parameter > to a different website, but they still get the "Access to Galaxy user > controls is disabled". > > I see it in lib/galaxy/webapps/galaxy/controllers/user.py, but I think at > that point its too late. > > > > On Tue, Sep 8, 2015 at 4:05 PM, Ryan G > wrote: > >> Yes, I have a test server I'm going to check this one. thanks for the >> link, that's perfect...I'll add some debugging code in here to see what's >> going on. >> >> On Tue, Sep 8, 2015 at 1:46 PM, Dannon Baker >> wrote: >> >>> Do you have a way to verify the "HTTP_MAIL" header is actually being >>> passed through your proxy server? >>> >>> The problem is that Galaxy still doesn't think it's receiving the >>> expected headers, so there isn't a good way that it can tell you more about >>> what might be going on. If you're able to tweak Galaxy (using a test >>> server) and add a few logging statements the code, this would be good >>> places to check what's going on (print the `environ` dictionary associated >>> with that request, along with self.remote_user_header to see what Galaxy is >>> actually trying to use): >>> >>> >>> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/framework/middleware/remoteuser.py#L49 >>> >>> -Dannon >>> >>> On Thu, Sep 3, 2015 at 1:51 PM, Ryan G >>> wrote: >>> >>>> It turns out our authentication system passes a header 'HTTP_MAIL' >>>> which contains the users email address. In galaxy.ini, I have >>>> >>>> use_remote_user = True >>>> remote_user_header = HTTP_MAIL >>>> >>>> After restarting,Galaxy still gives the same error. >>>> >>>> On Mon, Aug 31, 2015 at 3:44 PM, Dannon Baker >>>> wrote: >>>> >>>>> Hi Ryan, >>>>> >>>>> It may be that Galaxy is looking for a different remote user header >>>>> than your proxy is setting. I believe by default we look for >>>>> HTTP_REMOTE_USER, but this is configurable in galaxy.ini (so, you could >>>>> set >>>>> yours to HTTP_USER there). Let me know if this doesn't sort it out for >>>>> you >>>>> and we can dig deeper! >>>>> >>>>> -Dannon >>>>> >>>>> On Mon, Aug 31, 2015 at 3:42 PM, Ryan G >>>>> wrote: >>>>> >>>>>> Hi all - I'm trying to use external user authentication with Galaxy. >>>>>> The external authentication passes to Galaxy the username with the mail >>>>>> domain at HTTP_USER. >>>>>> >>>>>> In galaxy.ini, I enable: >>>>>> use_remote_user = True >>>>>> >>>>>> >>>>>> When I try to access Galaxy, I get the message: >>>>>> Galaxy is configured to authenticate users via an external method >>>>>> (such as HTTP authentication in Apache), but a username was not provided >>>>>> by >>>>>> the upstream (proxy) server. This is generally due to a misconfiguration >>>>>> in >>>>>> the upstream server. >>>>>> >>>>>> But nothing in paster.log indicating what the error is. >>>>>> >>>>>> How do I track this down? >>>>>> >>>>>> >>>>>> >>>>>> ___ >>>>>> Please keep all replies on the list by using "reply all" >>>>>> in your mail client. To manage your subscriptions to this >>>>>> and other Galaxy lists, please use the interface at: >>>>>> https://lists.galaxyproject.org/ >>>>>> >>>>>> To search Galaxy mailing lists use the unified search at: >>>>>> http://galaxyproject.org/search/mailinglists/ >>>>>> >>>>> >>>>> >>>> >>> >> > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] External User Authenticaion
Hi all - In regards to external user authentication that I have working now (see thread below). When users try to go to the actual Galaxy page, they get the message: Access to Galaxy is denied Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but no shared secret key was provided by the upstream (proxy) server. Please contact your local Galaxy administrator. The variable remote_user_secret and GX_SECRET header must be set before you may access Galaxy. That's fine and all but I'd like to have them redirected to the real login page. Is there a way to do this? I didn't see anything obvious and was thinking of adding a parameter to galaxy.ini and have Galaxy automatically forward them after 5 seconds or so. Ryan On Tue, Oct 13, 2015 at 10:49 AM, Ryan G wrote: > Hi all - In regards to external user authentication that I have working > now (see thread below). When users try to go to the actual Galaxy page, > they get the message: > > > On Thu, Oct 1, 2015 at 4:10 PM, Ryan G > wrote: > >> I finally got around to this and all is working well. I submitted 2 >> patches to remoteuser.py to assist in debugging incorrect set ups. >> >> Last question - When a user logs out, they get the page ""Access to >> Galaxy user controls is disabled". I've set the remote_user_logout_href >> parameter to a different website, but they still get the "Access to Galaxy >> user controls is disabled". >> >> I see it in lib/galaxy/webapps/galaxy/controllers/user.py, but I think at >> that point its too late. >> >> >> >> On Tue, Sep 8, 2015 at 4:05 PM, Ryan G >> wrote: >> >>> Yes, I have a test server I'm going to check this one. thanks for the >>> link, that's perfect...I'll add some debugging code in here to see what's >>> going on. >>> >>> On Tue, Sep 8, 2015 at 1:46 PM, Dannon Baker >>> wrote: >>> >>>> Do you have a way to verify the "HTTP_MAIL" header is actually being >>>> passed through your proxy server? >>>> >>>> The problem is that Galaxy still doesn't think it's receiving the >>>> expected headers, so there isn't a good way that it can tell you more about >>>> what might be going on. If you're able to tweak Galaxy (using a test >>>> server) and add a few logging statements the code, this would be good >>>> places to check what's going on (print the `environ` dictionary associated >>>> with that request, along with self.remote_user_header to see what Galaxy is >>>> actually trying to use): >>>> >>>> >>>> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/framework/middleware/remoteuser.py#L49 >>>> >>>> -Dannon >>>> >>>> On Thu, Sep 3, 2015 at 1:51 PM, Ryan G >>>> wrote: >>>> >>>>> It turns out our authentication system passes a header 'HTTP_MAIL' >>>>> which contains the users email address. In galaxy.ini, I have >>>>> >>>>> use_remote_user = True >>>>> remote_user_header = HTTP_MAIL >>>>> >>>>> After restarting,Galaxy still gives the same error. >>>>> >>>>> On Mon, Aug 31, 2015 at 3:44 PM, Dannon Baker >>>>> wrote: >>>>> >>>>>> Hi Ryan, >>>>>> >>>>>> It may be that Galaxy is looking for a different remote user header >>>>>> than your proxy is setting. I believe by default we look for >>>>>> HTTP_REMOTE_USER, but this is configurable in galaxy.ini (so, you could >>>>>> set >>>>>> yours to HTTP_USER there). Let me know if this doesn't sort it out for >>>>>> you >>>>>> and we can dig deeper! >>>>>> >>>>>> -Dannon >>>>>> >>>>>> On Mon, Aug 31, 2015 at 3:42 PM, Ryan G >>>>>> wrote: >>>>>> >>>>>>> Hi all - I'm trying to use external user authentication with >>>>>>> Galaxy. The external authentication passes to Galaxy the username with >>>>>>> the >>>>>>> mail domain at HTTP_USER. >>>>>>> >>>>>>> In galaxy.ini, I enable: >>>>>>> use_remote_user = True >>>>>>> >>>>>>> >>>>>>> Wh
Re: [galaxy-dev] User API keys with External (LDAP) authentication disabled?
Thanks Eric. Please excuse any typos -- Sent from my iPhone > On Oct 8, 2015, at 11:35 AM, Eric Rasche wrote: > > Howdy Ryan, > > The bug fix for this is now in Galaxy's dev branch, and I've opened a PR > to have it in the 15.10 release. This is the patch for your bug if you > need it sooner than the next release (assuming that PR gets merged). > https://patch-diff.githubusercontent.com/raw/galaxyproject/galaxy/pull/872.patch > > Ciao, > Eric > >> On 10/07/2015 04:43 PM, Eric Rasche wrote: >> Not from the admin interface right now. I noted this bug just the other >> day and intended to fix it as it applied to us as well. >> Until then, you can easily change the API key manually in the database. >> >> Cheers, >> Eric >> >> 2015-10-07 16:20 GMT-05:00 Ryan G > <mailto:ngsbioinformat...@gmail.com>>: >> >>Hi all - I have external authentication established with our >>enterprise wide LDAP working with Galaxy. I just noticed that I can >>no longer manage API keys for users from the Admin Page -> API >>Keys. I get "Access to Galaxy user controls is disabled. User >>controls are disabled when Galaxy is configured for external >>authentication" >> >>We basically have a 'nobody' user in Galaxy that populates the Data >>Library with new data from a proprietary system. We were using a >>user's API key (mine) to do this but want to switch over to a daemon >>style user key. In order to do so, I need to generate an API key >>for the dummy user. >> >>Is there no way to get API keys from the Admin interface with >>external authentication? >> >> >> >>___ >>Please keep all replies on the list by using "reply all" >>in your mail client. To manage your subscriptions to this >>and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >>To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> >> >> >> >> -- >> Eric Rasche >> Programmer II >> >> Center for Phage Technology >> Rm 312A, BioBio >> Texas A&M University >> College Station, TX 77843 >> 404-692-2048 >> e...@tamu.edu <mailto:e...@tamu.edu> > > -- > Eric Rasche > Programmer II > > Center for Phage Technology > Rm 312A, BioBio > Texas A&M University > College Station, TX 77843 > 404-692-2048 > e...@tamu.edu ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] User API keys with External (LDAP) authentication disabled?
Hi all - I have external authentication established with our enterprise wide LDAP working with Galaxy. I just noticed that I can no longer manage API keys for users from the Admin Page -> API Keys. I get "Access to Galaxy user controls is disabled. User controls are disabled when Galaxy is configured for external authentication" We basically have a 'nobody' user in Galaxy that populates the Data Library with new data from a proprietary system. We were using a user's API key (mine) to do this but want to switch over to a daemon style user key. In order to do so, I need to generate an API key for the dummy user. Is there no way to get API keys from the Admin interface with external authentication? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] External Pipeline Cleanup
Hi all - For various reasons, we've had to implement our pipelines external to Galaxy, but still give Galaxy the ability to run them. I've accomplished this by having the Galaxy tool wrapper call the external app to launch the pipelines. My problem is that when a user aborts the tool, the tool needs to be able to communicate to the pipeline that its need aborted. How can I do this? Is there some way to get a notification that the job has been cancelled before its actually cancelled to perform clean up? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] External User Authenticaion
I finally got around to this and all is working well. I submitted 2 patches to remoteuser.py to assist in debugging incorrect set ups. Last question - When a user logs out, they get the page ""Access to Galaxy user controls is disabled". I've set the remote_user_logout_href parameter to a different website, but they still get the "Access to Galaxy user controls is disabled". I see it in lib/galaxy/webapps/galaxy/controllers/user.py, but I think at that point its too late. On Tue, Sep 8, 2015 at 4:05 PM, Ryan G wrote: > Yes, I have a test server I'm going to check this one. thanks for the > link, that's perfect...I'll add some debugging code in here to see what's > going on. > > On Tue, Sep 8, 2015 at 1:46 PM, Dannon Baker > wrote: > >> Do you have a way to verify the "HTTP_MAIL" header is actually being >> passed through your proxy server? >> >> The problem is that Galaxy still doesn't think it's receiving the >> expected headers, so there isn't a good way that it can tell you more about >> what might be going on. If you're able to tweak Galaxy (using a test >> server) and add a few logging statements the code, this would be good >> places to check what's going on (print the `environ` dictionary associated >> with that request, along with self.remote_user_header to see what Galaxy is >> actually trying to use): >> >> >> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/framework/middleware/remoteuser.py#L49 >> >> -Dannon >> >> On Thu, Sep 3, 2015 at 1:51 PM, Ryan G >> wrote: >> >>> It turns out our authentication system passes a header 'HTTP_MAIL' which >>> contains the users email address. In galaxy.ini, I have >>> >>> use_remote_user = True >>> remote_user_header = HTTP_MAIL >>> >>> After restarting,Galaxy still gives the same error. >>> >>> On Mon, Aug 31, 2015 at 3:44 PM, Dannon Baker >>> wrote: >>> >>>> Hi Ryan, >>>> >>>> It may be that Galaxy is looking for a different remote user header >>>> than your proxy is setting. I believe by default we look for >>>> HTTP_REMOTE_USER, but this is configurable in galaxy.ini (so, you could set >>>> yours to HTTP_USER there). Let me know if this doesn't sort it out for you >>>> and we can dig deeper! >>>> >>>> -Dannon >>>> >>>> On Mon, Aug 31, 2015 at 3:42 PM, Ryan G >>>> wrote: >>>> >>>>> Hi all - I'm trying to use external user authentication with Galaxy. >>>>> The external authentication passes to Galaxy the username with the mail >>>>> domain at HTTP_USER. >>>>> >>>>> In galaxy.ini, I enable: >>>>> use_remote_user = True >>>>> >>>>> >>>>> When I try to access Galaxy, I get the message: >>>>> Galaxy is configured to authenticate users via an external method >>>>> (such as HTTP authentication in Apache), but a username was not provided >>>>> by >>>>> the upstream (proxy) server. This is generally due to a misconfiguration >>>>> in >>>>> the upstream server. >>>>> >>>>> But nothing in paster.log indicating what the error is. >>>>> >>>>> How do I track this down? >>>>> >>>>> >>>>> >>>>> ___ >>>>> Please keep all replies on the list by using "reply all" >>>>> in your mail client. To manage your subscriptions to this >>>>> and other Galaxy lists, please use the interface at: >>>>> https://lists.galaxyproject.org/ >>>>> >>>>> To search Galaxy mailing lists use the unified search at: >>>>> http://galaxyproject.org/search/mailinglists/ >>>>> >>>> >>>> >>> >> > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] External User Authenticaion
Yes, I have a test server I'm going to check this one. thanks for the link, that's perfect...I'll add some debugging code in here to see what's going on. On Tue, Sep 8, 2015 at 1:46 PM, Dannon Baker wrote: > Do you have a way to verify the "HTTP_MAIL" header is actually being > passed through your proxy server? > > The problem is that Galaxy still doesn't think it's receiving the expected > headers, so there isn't a good way that it can tell you more about what > might be going on. If you're able to tweak Galaxy (using a test server) > and add a few logging statements the code, this would be good places to > check what's going on (print the `environ` dictionary associated with that > request, along with self.remote_user_header to see what Galaxy is actually > trying to use): > > > https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/framework/middleware/remoteuser.py#L49 > > -Dannon > > On Thu, Sep 3, 2015 at 1:51 PM, Ryan G > wrote: > >> It turns out our authentication system passes a header 'HTTP_MAIL' which >> contains the users email address. In galaxy.ini, I have >> >> use_remote_user = True >> remote_user_header = HTTP_MAIL >> >> After restarting,Galaxy still gives the same error. >> >> On Mon, Aug 31, 2015 at 3:44 PM, Dannon Baker >> wrote: >> >>> Hi Ryan, >>> >>> It may be that Galaxy is looking for a different remote user header than >>> your proxy is setting. I believe by default we look for HTTP_REMOTE_USER, >>> but this is configurable in galaxy.ini (so, you could set yours to >>> HTTP_USER there). Let me know if this doesn't sort it out for you and we >>> can dig deeper! >>> >>> -Dannon >>> >>> On Mon, Aug 31, 2015 at 3:42 PM, Ryan G >>> wrote: >>> >>>> Hi all - I'm trying to use external user authentication with Galaxy. >>>> The external authentication passes to Galaxy the username with the mail >>>> domain at HTTP_USER. >>>> >>>> In galaxy.ini, I enable: >>>> use_remote_user = True >>>> >>>> >>>> When I try to access Galaxy, I get the message: >>>> Galaxy is configured to authenticate users via an external method (such >>>> as HTTP authentication in Apache), but a username was not provided by the >>>> upstream (proxy) server. This is generally due to a misconfiguration in the >>>> upstream server. >>>> >>>> But nothing in paster.log indicating what the error is. >>>> >>>> How do I track this down? >>>> >>>> >>>> >>>> ___ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> https://lists.galaxyproject.org/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>>> >>> >>> >> > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] External User Authenticaion
It turns out our authentication system passes a header 'HTTP_MAIL' which contains the users email address. In galaxy.ini, I have use_remote_user = True remote_user_header = HTTP_MAIL After restarting,Galaxy still gives the same error. On Mon, Aug 31, 2015 at 3:44 PM, Dannon Baker wrote: > Hi Ryan, > > It may be that Galaxy is looking for a different remote user header than > your proxy is setting. I believe by default we look for HTTP_REMOTE_USER, > but this is configurable in galaxy.ini (so, you could set yours to > HTTP_USER there). Let me know if this doesn't sort it out for you and we > can dig deeper! > > -Dannon > > On Mon, Aug 31, 2015 at 3:42 PM, Ryan G > wrote: > >> Hi all - I'm trying to use external user authentication with Galaxy. The >> external authentication passes to Galaxy the username with the mail domain >> at HTTP_USER. >> >> In galaxy.ini, I enable: >> use_remote_user = True >> >> >> When I try to access Galaxy, I get the message: >> Galaxy is configured to authenticate users via an external method (such >> as HTTP authentication in Apache), but a username was not provided by the >> upstream (proxy) server. This is generally due to a misconfiguration in the >> upstream server. >> >> But nothing in paster.log indicating what the error is. >> >> How do I track this down? >> >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] External User Authenticaion
Hi all - I'm trying to use external user authentication with Galaxy. The external authentication passes to Galaxy the username with the mail domain at HTTP_USER. In galaxy.ini, I enable: use_remote_user = True When I try to access Galaxy, I get the message: Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server. This is generally due to a misconfiguration in the upstream server. But nothing in paster.log indicating what the error is. How do I track this down? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy in Amazon
Hi all - We are running a local instance of Galaxy on our internal infrastructure. It seems to be going well. We've gotten to the point where we are ready to migrate our NGS data to Amazon for storage in S3. We are also looking at how Galaxy can be used in Amazon. Specifically, we are interested in understanding: 1) Should we run an instance of Galaxy in Amazon, or continue to run it locally (to minimize costs) but have it run analyses in Amazon? 2) Regardless of how we run it, data will be stored in S3. How will Galaxy interact with S3 for its Data Libraries? 3) Is it even possible to separate the Galaxy web interface from the HPC cluster? 3) We understand Galaxy in Amazon uses CloudMan. Can we run this in our VPC with our own AMI? If anyone can provide insights into how they are using Galaxy in Amazon, I am very interested to hear your thoughts. Ryan ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Workflow editor stuck on loading workflow
Hi - Yes, this is still happening. Clearing my browser's cache didn't help. I suspect this is related to a tool being removed/renamed that is used in the workflow, but not completely sure. Attached is the exported workflow. Let me know if you need anything else to help debug this. Thanks, Ryan On Mon, Jul 27, 2015 at 9:44 AM, John Chilton wrote: > Ryan - is this still a problem? I assume there is some use of dataset > collections in this workflow? What would be ideal is to determine a > minimum combination of data flow (connections) and tools that exhibit > this - and then share that workflow and tool with me. If you don't > have time for that - maybe just attempting to export the workflow and > sending it to me. I cannot make any promises but I can try to look it > over. > > Thanks for the bug report - we are doing a lot of work on workflows > and the workflow editor and if I encounter this bug and find a fix I > will let you know, > -John > > On Wed, Jul 15, 2015 at 4:18 PM, Ryan G > wrote: > > The error I see is "TypeError: c.effectiveMapOver is not a function" in > > static/scripts/galaxy.workflow_editor.canvas.js?v=1436897004 > > > > On Tue, Jul 14, 2015 at 4:50 PM, Björn Grüning < > bjoern.gruen...@gmail.com> > > wrote: > >> > >> Hi Ryan, > >> > >> try to look at the JS console. I suspect some problem with one of the > >> tools in your workflow. > >> > >> Cheers, > >> Bjoern > >> > >> Am 14.07.2015 um 22:02 schrieb Ryan G: > >> > Hmmm this only happens on a specific workflow. How can I debug this? > >> > > >> > On Tue, Jul 14, 2015 at 3:37 PM, Ryan G > >> > wrote: > >> > > >> >> It looks like a recent commit since 6/26 to 15.05 is break the > workflow > >> >> editor. I have a pipeline I'm trying to edit. I updated my instance > >> >> of > >> >> Galaxy and now when I try to edit a workflow, the editor is stuck at > >> >> "Loading workflow editor". > >> >> > >> >> > >> >> > >> > > >> > > >> > > >> > ___ > >> > Please keep all replies on the list by using "reply all" > >> > in your mail client. To manage your subscriptions to this > >> > and other Galaxy lists, please use the interface at: > >> > https://lists.galaxyproject.org/ > >> > > >> > To search Galaxy mailing lists use the unified search at: > >> > http://galaxyproject.org/search/mailinglists/ > >> > > > > > > > > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > Galaxy-Workflow-RNA-Seq_QC_(hg19)_Pipeline_v0.1.ga Description: Binary data ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error sorting or uploading Bam File
I would think the correct approach would be to allow any bam file and if a tool requires a coordinate sorted bam and one is not provided it would make sense for the tool to fail with an error. Does galaxy itself require a coordinate sorted bam or this this so the majority of tools can function properly? Sent from my iPhone > On Jul 17, 2015, at 11:08 AM, John Chilton wrote: > > I'm not the right person to respond to this but since no one else has > I will explain my limited (probably incorrect) understanding of the > problem and what needs to be done. I believe Galaxy assumes all bam > files are coordinated sorted by default - so Galaxy's bam datatype > would be better thought of as a coordinate-sorted bam. Certain people > do not want to allow non-coordinate sorted bam files because these > would be allowed by Galaxy as valid as inputs to tools that expect > sorted bams - and things would break. For the same reason I imagine > these people would argue the bai file needs to be generated because > certain tools will depend on its existence. > > I believe the proposed solution is to add an unsorted bam datatype to > Galaxy. I don't know if there is any work in progress on this but it > seems to be needed by many researchers. > > Hope this clarifies things somewhat, > -John > > >> On Mon, Jun 29, 2015 at 11:06 AM, julie dubois wrote: >> Hi all, >> >> My galaxy is the last update and I work with samtools 1.2. >> I have a bug with the sorting and the upload of bam file. >> This bug appears only when I try to upload bam sorted by name or when >> I try to sort by name. >> When I work with bam sorted by coordinate, there is no problem. >> >> So, when I try to sort a bam file by name, this error appears under >> the "bug icon" : >> >> Tool execution generated the following error message: >> [bam_sort_core] merging from 20 files... >> *** Error in `python': double free or corruption (!prev): 0x02897990 >> *** >> Aborted (core dumped) >> >> The tool produced the following additional output: >> >> [E::hts_idx_push] chromosome blocks not continuous >> Galaxy attempted to build the BAM index with samtools 1.0+ but failed: >> [Errno 2] No such file or directory: >> '/data/galaxy-dist/database/job_working_directory/024/24109/__dataset_48619_metadata_temp_file_MqhjBN.bai' >> >> And the same type of error appears when I try to upload bam sorted by name. >> >> >> What I understand is that the bam can be sorted properly (The command >> line to sort is ok in a terminal with no bug and I can follow this >> step in the job_working_directory during the run) but Galaxy seems to >> fail to create a bai. >> >> For our analysis pipeline, I think the bai is not crucial, is it >> possible to avoid this creation of bai during uploading and sorting of >> bam file by name ? >> >> Is there another problem than this creation of bai ? >> >> Thanks. >> >> Julie >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Workflow editor stuck on loading workflow
The error I see is "TypeError: c.effectiveMapOver is not a function" in static/scripts/galaxy.workflow_editor.canvas.js?v=1436897004 On Tue, Jul 14, 2015 at 4:50 PM, Björn Grüning wrote: > Hi Ryan, > > try to look at the JS console. I suspect some problem with one of the > tools in your workflow. > > Cheers, > Bjoern > > Am 14.07.2015 um 22:02 schrieb Ryan G: > > Hmmm this only happens on a specific workflow. How can I debug this? > > > > On Tue, Jul 14, 2015 at 3:37 PM, Ryan G > wrote: > > > >> It looks like a recent commit since 6/26 to 15.05 is break the workflow > >> editor. I have a pipeline I'm trying to edit. I updated my instance of > >> Galaxy and now when I try to edit a workflow, the editor is stuck at > >> "Loading workflow editor". > >> > >> > >> > > > > > > > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Workflow editor stuck on loading workflow
Hmmm this only happens on a specific workflow. How can I debug this? On Tue, Jul 14, 2015 at 3:37 PM, Ryan G wrote: > It looks like a recent commit since 6/26 to 15.05 is break the workflow > editor. I have a pipeline I'm trying to edit. I updated my instance of > Galaxy and now when I try to edit a workflow, the editor is stuck at > "Loading workflow editor". > > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Workflow editor stuck on loading workflow
It looks like a recent commit since 6/26 to 15.05 is break the workflow editor. I have a pipeline I'm trying to edit. I updated my instance of Galaxy and now when I try to edit a workflow, the editor is stuck at "Loading workflow editor". ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] galaxy.ini
It's in your config/ directory. Sent from my iPhone > On Jul 14, 2015, at 6:35 AM, Bryan Hepworth > wrote: > > Hi > > For the woefully inept, where in the heck is galaxy.ini stored? > > I saw the documentation that said change 127.0.0.1 to 0.0.0.0 and the file > name, can't find it to do so. > > I know it all works as I've installed a module and that all shows up and > works on localhost. > > Thanks > > Bryan > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy API to upload files to data library
Perfect. Thanks!
On Fri, Jun 26, 2015 at 6:02 PM, Martin Čech wrote:
> The second link leads to an endpoint that does exactly that.
> M.
>
>
> On Fri, Jun 26, 2015 at 4:43 PM Ryan G
> wrote:
>
>> What if the data is not in the history? Ie we received ngs data from an
>> external source and copied it to a location on our server. I now want to
>> link to it in Galaxy.
>>
>> What I was doing previously was entering the file system path through the
>> UX but we want to automate this a bit and have a script scan Various
>> directories and import all the *.fastq.gz files while preserving the
>> directory structure. I have most of the script written but just need to
>> figure out how to link to the datasets.
>>
>> Sent from my iPhone
>>
>> On Jun 26, 2015, at 1:24 PM, Martin Čech wrote:
>>
>> History Dataset Association. i.e. if you already have the dataset in
>> history you can very easily import it to a data library.
>>
>> M.
>>
>> On Fri, Jun 26, 2015 at 1:23 PM Ryan G
>> wrote:
>>
>>> What is HDA?
>>>
>>> Sent from my iPhone
>>>
>>> On Jun 26, 2015, at 1:10 PM, Martin Čech wrote:
>>>
>>> Hello Ryan,
>>>
>>> for interacting with libraries through the Bioblend:
>>>
>>> http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries
>>>
>>> for loading data to libraries form the Galaxy's system (e.g. after FTP
>>> upload, or when admin):
>>>
>>> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/lda_datasets.py#L401
>>>
>>> for uploading new files or importing from HDA:
>>>
>>> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/library_contents.py#L144
>>>
>>> Hope this helps.
>>>
>>> M.
>>>
>>> On Fri, Jun 26, 2015 at 12:56 PM Ryan G
>>> wrote:
>>>
>>>> By browsing the api code, I discovered library_contents.py that looks
>>>> like it should be used. Why this and not folder_contents.py? There seems
>>>> to be overlap of these two. I would expect to upload files to folders
>>>> within libraries...
>>>>
>>>>
>>>> On Thu, Jun 25, 2015 at 2:43 PM, Ryan G
>>>> wrote:
>>>>
>>>>> Hi all - I'm trying to figure out how to script the ability to upload
>>>>> data (fastq) files to Galaxy via the API.
>>>>>
>>>>> I can get the Library's root_folder_id, but am unsure of what the API
>>>>> call is to upload a file. I'm constructing this dictionary:
>>>>>
>>>>> data = {}
>>>>> data['folder_id'] = galaxyFolderId
>>>>> data['create_type'] = 'file'
>>>>> data['file_type'] = 'fastq'
>>>>> data['upload_option'] = 'upload_paths'
>>>>> data['filesystem_paths'] = fileToUpload
>>>>> data['link_data_only'] = 'link_to_files'
>>>>>
>>>>> I assume this is the correct format based on other code I've seen, but
>>>>> I'm not sure what the actual submit call should be. 'api/libraries/' or
>>>>> 'api/folders'
>>>>>
>>>>
>>>> ___
>>>> Please keep all replies on the list by using "reply all"
>>>> in your mail client. To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>> https://lists.galaxyproject.org/
>>>>
>>>> To search Galaxy mailing lists use the unified search at:
>>>> http://galaxyproject.org/search/mailinglists/
>>>
>>>
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Galaxy API to upload files to data library
What if the data is not in the history? Ie we received ngs data from an
external source and copied it to a location on our server. I now want to link
to it in Galaxy.
What I was doing previously was entering the file system path through the UX
but we want to automate this a bit and have a script scan Various directories
and import all the *.fastq.gz files while preserving the directory structure.
I have most of the script written but just need to figure out how to link to
the datasets.
Sent from my iPhone
> On Jun 26, 2015, at 1:24 PM, Martin Čech wrote:
>
> History Dataset Association. i.e. if you already have the dataset in history
> you can very easily import it to a data library.
>
> M.
>
>> On Fri, Jun 26, 2015 at 1:23 PM Ryan G wrote:
>> What is HDA?
>>
>> Sent from my iPhone
>>
>>> On Jun 26, 2015, at 1:10 PM, Martin Čech wrote:
>>>
>>> Hello Ryan,
>>>
>>> for interacting with libraries through the Bioblend:
>>> http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries
>>>
>>> for loading data to libraries form the Galaxy's system (e.g. after FTP
>>> upload, or when admin):
>>> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/lda_datasets.py#L401
>>>
>>> for uploading new files or importing from HDA:
>>> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/library_contents.py#L144
>>>
>>> Hope this helps.
>>>
>>> M.
>>>
>>>> On Fri, Jun 26, 2015 at 12:56 PM Ryan G
>>>> wrote:
>>>> By browsing the api code, I discovered library_contents.py that looks like
>>>> it should be used. Why this and not folder_contents.py? There seems to
>>>> be overlap of these two. I would expect to upload files to folders within
>>>> libraries...
>>>>
>>>>
>>>>> On Thu, Jun 25, 2015 at 2:43 PM, Ryan G
>>>>> wrote:
>>>>> Hi all - I'm trying to figure out how to script the ability to upload
>>>>> data (fastq) files to Galaxy via the API.
>>>>>
>>>>> I can get the Library's root_folder_id, but am unsure of what the API
>>>>> call is to upload a file. I'm constructing this dictionary:
>>>>>
>>>>> data = {}
>>>>> data['folder_id'] = galaxyFolderId
>>>>> data['create_type'] = 'file'
>>>>> data['file_type'] = 'fastq'
>>>>> data['upload_option'] = 'upload_paths'
>>>>> data['filesystem_paths'] = fileToUpload
>>>>> data['link_data_only'] = 'link_to_files'
>>>>>
>>>>> I assume this is the correct format based on other code I've seen, but
>>>>> I'm not sure what the actual submit call should be. 'api/libraries/' or
>>>>> 'api/folders'
>>>>
>>>> ___
>>>> Please keep all replies on the list by using "reply all"
>>>> in your mail client. To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>> https://lists.galaxyproject.org/
>>>>
>>>> To search Galaxy mailing lists use the unified search at:
>>>> http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy API to upload files to data library
What is HDA?
Sent from my iPhone
> On Jun 26, 2015, at 1:10 PM, Martin Čech wrote:
>
> Hello Ryan,
>
> for interacting with libraries through the Bioblend:
> http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries
>
> for loading data to libraries form the Galaxy's system (e.g. after FTP
> upload, or when admin):
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/lda_datasets.py#L401
>
> for uploading new files or importing from HDA:
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/library_contents.py#L144
>
> Hope this helps.
>
> M.
>
>> On Fri, Jun 26, 2015 at 12:56 PM Ryan G wrote:
>> By browsing the api code, I discovered library_contents.py that looks like
>> it should be used. Why this and not folder_contents.py? There seems to be
>> overlap of these two. I would expect to upload files to folders within
>> libraries...
>>
>>
>>> On Thu, Jun 25, 2015 at 2:43 PM, Ryan G wrote:
>>> Hi all - I'm trying to figure out how to script the ability to upload data
>>> (fastq) files to Galaxy via the API.
>>>
>>> I can get the Library's root_folder_id, but am unsure of what the API call
>>> is to upload a file. I'm constructing this dictionary:
>>>
>>> data = {}
>>> data['folder_id'] = galaxyFolderId
>>> data['create_type'] = 'file'
>>> data['file_type'] = 'fastq'
>>> data['upload_option'] = 'upload_paths'
>>> data['filesystem_paths'] = fileToUpload
>>> data['link_data_only'] = 'link_to_files'
>>>
>>> I assume this is the correct format based on other code I've seen, but I'm
>>> not sure what the actual submit call should be. 'api/libraries/' or
>>> 'api/folders'
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
___
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Re: [galaxy-dev] Galaxy API to upload files to data library
By browsing the api code, I discovered library_contents.py that looks like
it should be used. Why this and not folder_contents.py? There seems to be
overlap of these two. I would expect to upload files to folders within
libraries...
On Thu, Jun 25, 2015 at 2:43 PM, Ryan G wrote:
> Hi all - I'm trying to figure out how to script the ability to upload data
> (fastq) files to Galaxy via the API.
>
> I can get the Library's root_folder_id, but am unsure of what the API call
> is to upload a file. I'm constructing this dictionary:
>
> data = {}
> data['folder_id'] = galaxyFolderId
> data['create_type'] = 'file'
> data['file_type'] = 'fastq'
> data['upload_option'] = 'upload_paths'
> data['filesystem_paths'] = fileToUpload
> data['link_data_only'] = 'link_to_files'
>
> I assume this is the correct format based on other code I've seen, but I'm
> not sure what the actual submit call should be. 'api/libraries/' or
> 'api/folders'
>
___
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and other Galaxy lists, please use the interface at:
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[galaxy-dev] Galaxy API to upload files to data library
Hi all - I'm trying to figure out how to script the ability to upload data
(fastq) files to Galaxy via the API.
I can get the Library's root_folder_id, but am unsure of what the API call
is to upload a file. I'm constructing this dictionary:
data = {}
data['folder_id'] = galaxyFolderId
data['create_type'] = 'file'
data['file_type'] = 'fastq'
data['upload_option'] = 'upload_paths'
data['filesystem_paths'] = fileToUpload
data['link_data_only'] = 'link_to_files'
I assume this is the correct format based on other code I've seen, but I'm
not sure what the actual submit call should be. 'api/libraries/' or
'api/folders'
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] input dataset(s) and collections
If the user selects mulitple pairs of paired-end data, I want that submitted the same way as a list of paired-end data. I don't want a separate job for each paired-end data. Rather, I want a single job to consume the entire list. It seems to be easier to disable the ability to select multiple fastq1s and fastq2s, and only allow the user to specify a list of paired-end reads. This way, I can guarantee the pairs of fastq files match up correctly. On Thu, Jun 25, 2015 at 10:41 AM, John Chilton wrote: > So you don't want the multi-run options to appear next to these > inputs? There is currently no way for the tool author to disable this. > I will admit that I am skeptical this is a good idea, fundamentally is > feels like tool authors should not be able to prevent end users from > running the tool multiple times in parallel. Though I will also admit > in practice there are times this option leads to confusion for users > about what will actually happen and multiple people have requested an > option to disable it. > > > http://dev.list.galaxyproject.org/Tool-development-Selecting-a-single-item-from-input-dataset-td4666447.html > https://trello.com/c/qCtBBB8n > > -John > > > On Tue, Jun 23, 2015 at 12:58 PM, Ryan G > wrote: > > Hi all - I'm constructing a wrapper for a tool I have and the input to > the > > tool can be: > > > > 1) a single fastq file (single end sample) > > 2) multiple singled-end fastq files > > 3) a single paired-end sample > > 4) multiple paired-end samples. > > > > I have cases #1 and #2 handled, however case #3 is presenting a > problem. If > > the user select "Paired-End" sample, I want to restrict them to selecting > > only a single fastq1 and fastq2 file. > > > > If they want to submit multiple paired-end samples I only want to allow > them > > to submit them as a list of dataset pairs. I can get this part to work. > > > > I just need to restrict users to selecting only a single fastq1 and > fastq2 > > file when the input_type is Paired-End. > > > > My XML is as follows. Any help would be appreciated > > > > > > > > > > Single-End > > Paired-End > > Paired Collection > > > > > > label="Select > > fastq dataset" multiple="true" help="Specify dataset with single end > reads" > > /> > > > > > > label="Select > > fastq dataset" help="Specify dataset with 1st of paired-end reads" /> > > label="Select > > fastq dataset" help="Specify dataset with 2nd of paired-end reads" /> > > > > > > > collection_type="list:paired" label="Select a paired collection" > help="See > > help section for an explanation of dataset collections"/> > > > > > > > > > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] bowtie dataset pair input
Hi all - It looks like bowtie's wrapper is working incorrectly for a list of dataset pairs. Its expecting all the forward reads in one dataset list and the reverse reads in a separate dataset list. Instead, I have a list of dataset pairs (for paired-end data). This cannot be provided to bowtie as input. If I correct this, should I create a pull request for it? Alternatively, does someone already have a corrected version of this? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] input dataset(s) and collections
Hi all - I'm constructing a wrapper for a tool I have and the input to the tool can be: 1) a single fastq file (single end sample) 2) multiple singled-end fastq files 3) a single paired-end sample 4) multiple paired-end samples. I have cases #1 and #2 handled, however case #3 is presenting a problem. If the user select "Paired-End" sample, I want to restrict them to selecting only a single fastq1 and fastq2 file. If they want to submit multiple paired-end samples I only want to allow them to submit them as a list of dataset pairs. I can get this part to work. I just need to restrict users to selecting only a single fastq1 and fastq2 file when the input_type is Paired-End. My XML is as follows. Any help would be appreciated Single-End Paired-End Paired Collection ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Custom Tool Dev Questions
Ok, Great. I think I have part of this figured out. I have a conditional input as specified: Single-End Paired-End Paired Collection In my section, I want to test how this is passed to the tool, so I have: #if str( $input_type.input_type_selector ) == "single": echo "Input Type: Single" echo "Input File: $input_type.fastq_input1" #elif str( $input_type.input_type_selector ) == "paired": echo "Input Type: Paired" echo "FastQ1: $input_type.fastq_input1\nFastQ2: $input_type.fastq_input2" #elif str( $input_type.input_type_selector ) == "paired_collection": print "Input Type: Collection\n" #for $element in $input_type.$fastq_collection: echo "FastQ1: $element.fastq_input1" #end for #end if The "single" and "paired" works as expected, however I can select multiple input for "paired" which I don't want to allow. A user should only be able to select a single pair of fastq files. To select multiple pairs, I have "paired_collection". The second problem is in the command section, I'm trying to iterated through the pair of inputs, however my echo statement is causing a Cheetah error. I tried different incarnations of it as well. My latest (and what I thought correct) is shown above. It generates the error: Traceback (most recent call last): File "/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/jobs/runners/__init__.py", line 163, in prepare_job job_wrapper.prepare() File "/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/jobs/__init__.py", line 858, in prepare self.command_line, self.extra_filenames = tool_evaluator.build() File "/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/tools/evaluation.py", line 411, in build self.__build_command_line( ) File "/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/tools/evaluation.py", line 427, in __build_command_line command_line = fill_template( command, context=param_dict ) File "/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1434732603_97_56713.py", line 107, in respond AttributeError: 'dict' object has no attribute 'VFFSL' How do I iterate through the fastq inputs when they are passed as a list:paired? On Fri, Jun 19, 2015 at 11:31 AM, John Chilton wrote: > The option in the GUI for selecting multiple datasets for a single > data parameter - causes multiple jobs to be created as you noted. If > you just place multiple="true" on your data input parameter - that > button will go away and all the datasets will be used for a single > job. > > If your tool consumes pairs of datasets - you will want to expose an > option where you are using a parameter like: > > collection_type="list:paired" format="fastq" /> > > and then your users will have to use the data collection creator to > pair off the datasets into a big list before using your tool - but the > creator is actually really nice - I think it makes it very easy to > build large lists of pairs. > > Hope this helps - happy to provide more details, > -John > > On Fri, Jun 19, 2015 at 11:24 AM, Ryan G > wrote: > > Hi all - I have a tool which is essentially an entire NGS pipeline > bundled > > into a perl script and associated modules. I'd like to offer this tool > to > > users via Galaxy. > > > > I'm trying to pass a bunch of fastq files to the tool, but noticed that > > operating on multiple datasets creates a separate job for each dataset. > I > > want to pass all the datasets to the tool so only one galaxy job is > actually > > created. Is this possible, and if so, how do I go about doing this? > > > > Ryan > > > > > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Custom Tool Dev Questions
Hi all - I have a tool which is essentially an entire NGS pipeline bundled into a perl script and associated modules. I'd like to offer this tool to users via Galaxy. I'm trying to pass a bunch of fastq files to the tool, but noticed that operating on multiple datasets creates a separate job for each dataset. I want to pass all the datasets to the tool so only one galaxy job is actually created. Is this possible, and if so, how do I go about doing this? Ryan ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Bug in commit 38679a0
In scripts/functional_tests.py, line 71, the change is causing a directory called "test-data,https://github.com/galaxyproject/galaxy- test-data.git" to get created. I'm not sure that's the intention of this fix. default_galaxy_test_file_dir is assigned to test_dir, then never used again. test_dir is used to create the testing directory. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] functional tests / database lock
Thanks. Let me know how I can help. On Wed, Jun 17, 2015 at 12:08 PM, Dannon Baker wrote: > Thanks, I'll take a look. Non-tool-based functional tests should *not* > fail out of the box, and we'll fix them :) > > On Wed, Jun 17, 2015 at 12:04 PM Ryan G > wrote: > >> All the functional.test_admin_features >> Most of the functional.test_data_security >> functional.test_history_functions >> >> I'm attaching a PDF printout of the run_functional_tests.html >> >> >> >> On Wed, Jun 17, 2015 at 12:01 PM, Dannon Baker >> wrote: >> >>> Which tests are failing, specifically? Many tests will fail without the >>> underlying tools installed. >>> >>> On Wed, Jun 17, 2015 at 12:01 PM Ryan G >>> wrote: >>> >>>> I've migrated my staging instance to use postgres and ran the >>>> functional tests. I see lots failing. I know this is known and perhaps >>>> expected, but it still bothers me. I would expect to see all the tests >>>> pass on a clean instance. If the tests aren't passing, to me, that >>>> indicates a problem somewhere. What's the point in having the tests if >>>> they always fail? >>>> >>>> >>>> >>>> On Tue, Jun 16, 2015 at 1:12 PM, Ryan G >>>> wrote: >>>> >>>>> I am using postgres in production but want to validate my staging >>>>> instance before pushing it into production. I do this with the functional >>>>> tests. I guess I'll have to set up a postgres database for the staging >>>>> instance as well. >>>>> >>>>> >>>>> On Mon, Jun 15, 2015 at 10:32 AM, John Chilton >>>>> wrote: >>>>> >>>>>> Not exactly - I feel like sqlite should be able to do the kinds of >>>>>> things Galaxy does without this occurring - it should just be >>>>>> inefficient. We are probably doing something across multiple threads >>>>>> that we should not be - presumably related to job handling. After a >>>>>> recent sqlalchemy upgrade - there is now a new error message in the >>>>>> logs that should help track down the problem: >>>>>> >>>>>> sqlalchemy.pool.NullPool ERROR 2015-06-15 09:53:47,547 Exception >>>>>> during reset or similar >>>>>> Traceback (most recent call last): >>>>>> File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 571, in >>>>>> _finalize_fairy >>>>>> fairy._reset(pool) >>>>>> File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 705, >>>>>> in _reset >>>>>> pool._dialect.do_rollback(self) >>>>>> File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", >>>>>> line 412, in do_rollback >>>>>> dbapi_connection.rollback() >>>>>> ProgrammingError: SQLite objects created in a thread can only be used >>>>>> in that same thread.The object was created in thread id >>>>>> 140442561648384 and this is thread id 140442989479680 >>>>>> >>>>>> At any rate - we recommend using postgres in production for a reason - >>>>>> these sqlite errors are pretty common. >>>>>> >>>>>> -John >>>>>> >>>>>> >>>>>> On Fri, Jun 12, 2015 at 11:15 AM, Ryan G >>>>>> wrote: >>>>>> > Is there a known cause for this? >>>>>> > >>>>>> > On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo < >>>>>> nsora...@tiscali.it> >>>>>> > wrote: >>>>>> >> >>>>>> >> Hi Ryan, >>>>>> >> there is no know fix for this, apart from moving to PostgreSQL. >>>>>> >> >>>>>> >> Cheers, >>>>>> >> Nicola >>>>>> >> >>>>>> >> Il 12.06.2015 16:43 Ryan G ha scritto: >>>>>> >> >>>>>> >> Hi all - I'm running functional tests on a set of tools using >>>>>> >> 'run_tests.sh -sid ...'. A few of the tests fail. When I go back >>>>>> and run >>>>>> >> the tool tests individually, they succeed
Re: [galaxy-dev] functional tests / database lock
I've migrated my staging instance to use postgres and ran the functional tests. I see lots failing. I know this is known and perhaps expected, but it still bothers me. I would expect to see all the tests pass on a clean instance. If the tests aren't passing, to me, that indicates a problem somewhere. What's the point in having the tests if they always fail? On Tue, Jun 16, 2015 at 1:12 PM, Ryan G wrote: > I am using postgres in production but want to validate my staging instance > before pushing it into production. I do this with the functional tests. I > guess I'll have to set up a postgres database for the staging instance as > well. > > > On Mon, Jun 15, 2015 at 10:32 AM, John Chilton > wrote: > >> Not exactly - I feel like sqlite should be able to do the kinds of >> things Galaxy does without this occurring - it should just be >> inefficient. We are probably doing something across multiple threads >> that we should not be - presumably related to job handling. After a >> recent sqlalchemy upgrade - there is now a new error message in the >> logs that should help track down the problem: >> >> sqlalchemy.pool.NullPool ERROR 2015-06-15 09:53:47,547 Exception >> during reset or similar >> Traceback (most recent call last): >> File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 571, in >> _finalize_fairy >> fairy._reset(pool) >> File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 705, in >> _reset >> pool._dialect.do_rollback(self) >> File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", >> line 412, in do_rollback >> dbapi_connection.rollback() >> ProgrammingError: SQLite objects created in a thread can only be used >> in that same thread.The object was created in thread id >> 140442561648384 and this is thread id 140442989479680 >> >> At any rate - we recommend using postgres in production for a reason - >> these sqlite errors are pretty common. >> >> -John >> >> >> On Fri, Jun 12, 2015 at 11:15 AM, Ryan G >> wrote: >> > Is there a known cause for this? >> > >> > On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo >> > wrote: >> >> >> >> Hi Ryan, >> >> there is no know fix for this, apart from moving to PostgreSQL. >> >> >> >> Cheers, >> >> Nicola >> >> >> >> Il 12.06.2015 16:43 Ryan G ha scritto: >> >> >> >> Hi all - I'm running functional tests on a set of tools using >> >> 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and >> run >> >> the tool tests individually, they succeed. So I looked into why they >> fail >> >> when running them in batch, and it turns out to be a database lock. >> I'm >> >> using the default sqllite database that run_tests.sh creates. Does >> this >> >> need to be tuned somehow? >> >> >> >> >> >> galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched >> >> Error - : (OperationalError) database is locked u'SELECT api_keys.id >> AS >> >> api_keys_id, api_keys.create_time AS api_keys_create_time, >> api_keys.user_id >> >> AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys >> \nWHERE >> >> api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) >> >> URL: >> >> >> http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746714beb6212bc8 >> >> File >> >> >> '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py', >> >> line 149 in __call__ >> >> app_iter = self.application(environ, sr_checker) >> >> File >> >> >> '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', >> >> line 84 in __call__ >> >> return self.application(environ, start_response) >> >> File >> >> >> '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', >> >> line 633 in __call__ >> >> return self.application(environ, start_response) >> >> File >> >> >> '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', >> >> line 132 in __call__ >> >> return self.handle_request( environ, start_response ) >> >> File
Re: [galaxy-dev] functional tests / database lock
I am using postgres in production but want to validate my staging instance before pushing it into production. I do this with the functional tests. I guess I'll have to set up a postgres database for the staging instance as well. On Mon, Jun 15, 2015 at 10:32 AM, John Chilton wrote: > Not exactly - I feel like sqlite should be able to do the kinds of > things Galaxy does without this occurring - it should just be > inefficient. We are probably doing something across multiple threads > that we should not be - presumably related to job handling. After a > recent sqlalchemy upgrade - there is now a new error message in the > logs that should help track down the problem: > > sqlalchemy.pool.NullPool ERROR 2015-06-15 09:53:47,547 Exception > during reset or similar > Traceback (most recent call last): > File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 571, in > _finalize_fairy > fairy._reset(pool) > File "build/bdist.linux-x86_64/egg/sqlalchemy/pool.py", line 705, in > _reset > pool._dialect.do_rollback(self) > File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", > line 412, in do_rollback > dbapi_connection.rollback() > ProgrammingError: SQLite objects created in a thread can only be used > in that same thread.The object was created in thread id > 140442561648384 and this is thread id 140442989479680 > > At any rate - we recommend using postgres in production for a reason - > these sqlite errors are pretty common. > > -John > > > On Fri, Jun 12, 2015 at 11:15 AM, Ryan G > wrote: > > Is there a known cause for this? > > > > On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo > > wrote: > >> > >> Hi Ryan, > >> there is no know fix for this, apart from moving to PostgreSQL. > >> > >> Cheers, > >> Nicola > >> > >> Il 12.06.2015 16:43 Ryan G ha scritto: > >> > >> Hi all - I'm running functional tests on a set of tools using > >> 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and > run > >> the tool tests individually, they succeed. So I looked into why they > fail > >> when running them in batch, and it turns out to be a database lock. I'm > >> using the default sqllite database that run_tests.sh creates. Does this > >> need to be tuned somehow? > >> > >> > >> galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched > >> Error - : (OperationalError) database is locked u'SELECT api_keys.id AS > >> api_keys_id, api_keys.create_time AS api_keys_create_time, > api_keys.user_id > >> AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys > \nWHERE > >> api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) > >> URL: > >> > http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746714beb6212bc8 > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py', > >> line 149 in __call__ > >> app_iter = self.application(environ, sr_checker) > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', > >> line 84 in __call__ > >> return self.application(environ, start_response) > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', > >> line 633 in __call__ > >> return self.application(environ, start_response) > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', > >> line 132 in __call__ > >> return self.handle_request( environ, start_response ) > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', > >> line 159 in handle_request > >> trans = self.transaction_factory( environ ) > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', > >> line 71 in > >> self.set_transaction_factory( lambda e: self.transaction_chooser( e, > >> galaxy_app, session_cookie ) ) > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', > >> line 102 in transaction_chooser > >> return GalaxyWebTransaction( environ, galaxy_app, self, > session_cookie ) > >> File > >> > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/w
Re: [galaxy-dev] picard_MarkDuplicatesWithMateCigar functional test failure
done
On Fri, Jun 12, 2015 at 11:33 AM, Nicola Soranzo
wrote:
> Hi Ryan,
> please open a pull request at
> https://github.com/galaxyproject/tools-devteam
>
> The file is in tools/picard/ directory.
>
> Thanks,
> Nicola
>
> Il 12.06.2015 17:23 Ryan G ha scritto:
>
> The functional test for this tool fails. Looking at the XML wrapper, it
> looks like $comments is invalidit doesn't exist anywhere else in the
> xml file. I know that comments can be specified multiple times however
> there is no way to get the comments fields to appear multiple times in the
> UI as far as I can tell. So, I changed it from
>
> #for $element in $comments:
> COMMENT="${element.comment}"
> #end for
>
> to
>
> COMMENT="${comment}"
>
> and the functional test passes.
>
>
>
>
>
>
>
>
> Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate,
> le video chiamate e persino le chiamate di gruppo.
> E chiami gratis anche i numeri fissi e mobili nel mondo!
> Scarica subito l’app Vai su https://www.indoona.com/
>
>
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Re: [galaxy-dev] keep job output and scripts on failed tests
I tried that and the directories don't get removed however the job files still get deleted. On Fri, Jun 12, 2015 at 12:03 PM, Peter Cock wrote: > Hi Ryan, > > Something very handy for tool developers running functional tests > is if the environment variable GALAXY_TEST_NO_CLEANUP > is set, run_tests.sh shouldn't remove the test output. > > This is great when debugging why a test is failing. > > Peter > > > On Fri, Jun 12, 2015 at 4:29 PM, Ryan G > wrote: > > I'd like to recommend a change. If jobs fail to run during functional > > tests, I'd like to keep the failed job files around to be examined. I > added > > the following to do so: > > > > +++ scripts/functional_tests.py > > @@ -372,6 +372,7 @@ def main(): > > user_library_import_dir=user_library_import_dir, > > master_api_key=master_api_key, > > use_tasked_jobs=True, > > + cleanup_job='onsuccess' > > ) > > if install_database_connection is not None: > > kwargs[ 'install_database_connection' ] = > > install_database_connection > > > > > > > > > > > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] keep job output and scripts on failed tests
I'd like to recommend a change. If jobs fail to run during functional tests, I'd like to keep the failed job files around to be examined. I added the following to do so: +++ scripts/functional_tests.py @@ -372,6 +372,7 @@ def main(): user_library_import_dir=user_library_import_dir, master_api_key=master_api_key, use_tasked_jobs=True, + cleanup_job='onsuccess' ) if install_database_connection is not None: kwargs[ 'install_database_connection' ] = install_database_connection ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] picard_MarkDuplicatesWithMateCigar functional test failure
The functional test for this tool fails. Looking at the XML wrapper, it
looks like $comments is invalidit doesn't exist anywhere else in the
xml file. I know that comments can be specified multiple times however
there is no way to get the comments fields to appear multiple times in the
UI as far as I can tell. So, I changed it from
#for $element in $comments:
COMMENT="${element.comment}"
#end for
to
COMMENT="${comment}"
and the functional test passes.
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Re: [galaxy-dev] functional tests / database lock
Is there a known cause for this? On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo wrote: > Hi Ryan, > there is no know fix for this, apart from moving to PostgreSQL. > > Cheers, > Nicola > > Il 12.06.2015 16:43 Ryan G ha scritto: > > Hi all - I'm running functional tests on a set of tools using > 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and run > the tool tests individually, they succeed. So I looked into why they fail > when running them in batch, and it turns out to be a database lock. I'm > using the default sqllite database that run_tests.sh creates. Does this > need to be tuned somehow? > > > galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched > Error - : (OperationalError) database is locked u'SELECT api_keys.id AS > api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id > AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE > api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) > URL: > http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746714beb6212bc8 > File > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py', > line 149 in __call__ > app_iter = self.application(environ, sr_checker) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', > line 84 in __call__ > return self.application(environ, start_response) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', > line 633 in __call__ > return self.application(environ, start_response) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', > line 132 in __call__ > return self.handle_request( environ, start_response ) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', > line 159 in handle_request > trans = self.transaction_factory( environ ) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', > line 71 in > self.set_transaction_factory( lambda e: self.transaction_chooser( e, > galaxy_app, session_cookie ) ) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', > line 102 in transaction_chooser > return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', > line 194 in __init__ > self.error_message = self._authenticate_api( session_cookie ) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', > line 283 in _authenticate_api > provided_key = self.sa_session.query( self.app.model.APIKeys ).filter( > self.app.model.APIKeys.table.c.key == api_key ).one() > File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184 in > one > File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2227 in > __iter__ > File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242 in > _execute_and_instances > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1449 > in execute > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1584 > in _execute_clauseelement > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1698 > in _execute_context > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1691 > in _execute_context > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py', line 331 > in do_execute > OperationalError: (OperationalError) database is locked u'SELECT > api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time, > api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM > api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) > > > > > > Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, > le video chiamate e persino le chiamate di gruppo. > E chiami gratis anche i numeri fissi e mobili nel mondo! > Scarica subito l’app Vai su https://www.indoona.com/ > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] functional tests / database lock
Hi all - I'm running functional tests on a set of tools using 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and run the tool tests individually, they succeed. So I looked into why they fail when running them in batch, and it turns out to be a database lock. I'm using the default sqllite database that run_tests.sh creates. Does this need to be tuned somehow? galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched Error - : (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) URL: http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746714beb6212bc8 File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 159 in handle_request trans = self.transaction_factory( environ ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 71 in self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 102 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 194 in __init__ self.error_message = self._authenticate_api( session_cookie ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 283 in _authenticate_api provided_key = self.sa_session.query( self.app.model.APIKeys ).filter( self.app.model.APIKeys.table.c.key == api_key ).one() File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184 in one File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2227 in __iter__ File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242 in _execute_and_instances File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1449 in execute File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1584 in _execute_clauseelement File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1698 in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1691 in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py', line 331 in do_execute OperationalError: (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Feature Request: Ability to specify a directory to read xml files for tool configuration
Thank you John and Bjoern. I will take a look at both. On Thu, Jun 11, 2015 at 1:35 PM, John Chilton wrote: > Ryan, > > This is possible using the relatively new tool_dir tag. > > > > This still looks in the tool path like other the normal tool tag. > > -John > > > On Thu, Jun 11, 2015 at 1:16 PM, Björn Grüning > wrote: > > Hi Ryan, > > > > have you looked at this option? > > > > # Set to True to enable monitoring of tools and tool directories > > # listed in any tool config file specified in tool_config_file option. > > # If changes are found, tools are automatically reloaded. Watchdog ( > > # https://pypi.python.org/pypi/watchdog ) must be installed and > > # available to Galaxy to use this option. Other options include 'auto' > > # which will attempt to watch tools if the watchdog library is available > > # but won't fail to load Galaxy if it is not and 'polling' which will use > > # a less efficient monitoring scheme that may work in wider range of > > scenarios > > # than the watchdog default. > > #watch_tools = False > > > > Cheers, > > Bjoern > > > > > > Am 11.06.2015 um 18:09 schrieb Ryan G: > >> Right now for each tool I have, I have to list the xml file per tool in > >> tool_conf.xml. I'd like to specify a directory that Galaxy will scan > for a > >> list of xml files and load all of them. So instead of: > >> > >> > >> > >> > >> > >> > >> > >> I can do: > >> > >> > >> > >> > >> > >> I'd add this to Trello but unfortunately my company blocks the site. > >> > >> > >> > >> ___ > >> Please keep all replies on the list by using "reply all" > >> in your mail client. To manage your subscriptions to this > >> and other Galaxy lists, please use the interface at: > >> https://lists.galaxyproject.org/ > >> > >> To search Galaxy mailing lists use the unified search at: > >> http://galaxyproject.org/search/mailinglists/ > >> > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Feature Request: Ability to specify a directory to read xml files for tool configuration
Right now for each tool I have, I have to list the xml file per tool in tool_conf.xml. I'd like to specify a directory that Galaxy will scan for a list of xml files and load all of them. So instead of: I can do: I'd add this to Trello but unfortunately my company blocks the site. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Functional Test Failures with 15.05
Hi - Are the functional tests for Galaxy supposed to run out of the box? I'm getting lots a failures with a fresh install in a virtual python environment. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] minor visual bug found when using Firefox
In the workflow editor, if you add an Input dataset collection, the "Collection Type:" shows list. No dropdown arrow appears using Firefox. A dropdown arrow appears when you mouse over using Chrome. In Firefox, if you mouse over where the dropdown box should be, you can still click to choose "list of datasets..." For the longest time, I thought this was broken until a co-worker showed me it works with Chrome. I'd make a Trello card for this but I can't access Trello from behind the company firewall ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Can a tool retrieve a user's API KEY?
I'm trying to create a tool that user's can use that will interact with Galaxy 's API, however the tool needs to be able to determine the user's API key.Is this possible? Can a tool determine what the user's API key is when the user actually runs the tool? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed
You are correct. It's always passing even when it fails. There was nothing in the docs to indicate a pass. Sent from my iPhone > On Apr 28, 2015, at 3:44 PM, John Chilton wrote: > > I feel like that stdio tag is going to cause it to always pass - even > if the exit code is not 0. Am I wrong? I like: > > > > > > myself. Björn Grüning uses - > > > > > > > > > which is a popular choice. > > As a heads up for people reading discussion in the future - starting > in 15.05 - you will be able to just add detect_errors="exit_code" on > the command tag to get a more sensible default behavior. > https://github.com/galaxyproject/galaxy/pull/117 > > -John > > >> On Tue, Apr 28, 2015 at 12:12 PM, Ryan G wrote: >> >> >> >> >> >> this works. Thanks. >> >> On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker >> wrote: >>> >>> Like Peter mentions, we did this because historically not all tools used >>> (still don't, I guess) exit codes correctly. If yours does, you can set >>> exit_code tags and everything should work. >>> >>> On Tue, Apr 28, 2015 at 11:47 AM Ryan G >>> wrote: >>>> >>>> ok, thanks. Let me look at this. When I look at the information about >>>> the tool, Galaxy does see the exit code is 0, which I think would be >>>> sufficient to know the tool ran correctly. >>>> >>>> >>>> On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock >>>> wrote: >>>>> >>>>> You probably need to set the tag, since due to a >>>>> historical design choice by default any output on stderr >>>>> is treated as an error. See: >>>>> >>>>> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax >>>>> >>>>> Peter >>>>> >>>>> On Tue, Apr 28, 2015 at 4:41 PM, Ryan G >>>>> wrote: >>>>>> Hi - I implemented a tool I us into Galaxy but when I run the tool >>>>>> view >>>>>> Galaxy, Galaxy thinks the tool failed. I checked the output file the >>>>>> tools >>>>>> create, and it succeeded. >>>>>> >>>>>> How do I tell Galaxy that a tool it ran was successful? Is it >>>>>> something in >>>>>> my XML file? The tool is outputting some info to stderr. Could this >>>>>> be >>>>>> why? >>>>>> >>>>>> ___ >>>>>> Please keep all replies on the list by using "reply all" >>>>>> in your mail client. To manage your subscriptions to this >>>>>> and other Galaxy lists, please use the interface at: >>>>>> https://lists.galaxyproject.org/ >>>>>> >>>>>> To search Galaxy mailing lists use the unified search at: >>>>>> http://galaxyproject.org/search/mailinglists/ >>>> >>>> >>>> ___ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> https://lists.galaxyproject.org/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >> >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Data Libraries
We have 4 different people in our sequencing lab each working on different projects. Once sequencing is done, they want to be able to create a data library specific for that project. Giving them all admin rights is not what we want, but instead giving them the ability to add data libraries so that the PI's and analysts can get access to the data is preferable. Creating one library and allowing them to add subfolders basically forces all the data into 1 library. -- won't work. Having somone with admin rights create a library and give them access to it could work but isn't preferable as that creates unnecessary steps for an admin person that isn't really needed. One only other option is to give them a tool that creates the library for them, but this is a workaround. On Fri, Apr 24, 2015 at 7:28 AM, Nicola Soranzo wrote: > You may just use a different folder for each project inside a > "Sequencing" library. Would that work? > > Nicola > > Il 24.04.2015 13:10 Ryan G ha scritto: > > This could work. In the long run though, after sequencing for a project, > we'd like them people in the sequencing lab to be able to add the data to > Galaxy in project specific libraries, without having an admin create a > library for them. > > On Thu, Apr 23, 2015 at 4:56 PM, Martin Čech wrote: > >> Hello Ryan, >> it is currently not possible to give users rights to create data >> libraries. However you can create the libraries for them and give them >> rights to create and manage subfolders (doing the same things but one level >> below). >> Would that address your goal? >> Martin >> >> On Thu, Apr 23, 2015 at 4:33 PM Ryan G >> wrote: >> >>> Hi all - We are trying to use Galaxy as a mechanism for our sequencing >>> lab to create data libraries for data they generate. I noticed in the >>> docs, only Admins are able to create data libraries. Is there a way to >>> change this? I'd like to give specific users in our group this ability >>> without giving them admin rights. >>> >>> Ryan >>> >>> ___ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >> >> > > > Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, > le video chiamate e persino le chiamate di gruppo. > E chiami gratis anche i numeri fissi e mobili nel mondo! > Scarica subito l’app Vai su https://www.indoona.com/ > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] optional tool arguments
Yes it took some experimenting but I finally figured it out. Sent from my iPhone > On Apr 29, 2015, at 4:51 AM, Peter Cock wrote: > > Yes, for example: > https://github.com/peterjc/pico_galaxy/blob/master/tools/seq_filter_by_id/seq_filter_by_id.xml > > Peter > >> On Wed, Apr 29, 2015 at 8:23 AM, Hans-Rudolf Hotz wrote: >> Hi Ryan >> >> I guess you can work with filters, see: >> >> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_set >> >> >> >> Regards, Hans-Rudolf >> >> >> >> >>> On 04/28/2015 06:28 PM, Ryan G wrote: >>> >>> Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or >>> 2 fastq files as input. If 1 file is specified, then 1 output file is >>> created. If 2 inputs are specified, then 2 output files will be >>> created. How do I specify the optional output parameter? >>> >>> I'm using this as my tool description right now: >>> >>> >>> a fastq file >>> >>> ### Check for optional input file >>> #if strlen($fq2) > 0: >>> RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o >>> $out2 >>> #else: >>> RandomSubFq -w $readsRequested -i "$fq1" -o $out1 >>> #end if >>> >>> >>> >>> >>> >> label="Total number of reads you want from the file"/> >>> >>> >>> >>> >>> >>> >>> >> /> >>> >>> >>> >>> >>> >>> ___ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] optional tool arguments
Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or 2 fastq files as input. If 1 file is specified, then 1 output file is created. If 2 inputs are specified, then 2 output files will be created. How do I specify the optional output parameter? I'm using this as my tool description right now: a fastq file ### Check for optional input file #if strlen($fq2) > 0: RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o $out2 #else: RandomSubFq -w $readsRequested -i "$fq1" -o $out1 #end if ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed
this works. Thanks. On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker wrote: > Like Peter mentions, we did this because historically not all tools used > (still don't, I guess) exit codes correctly. If yours does, you can set > exit_code tags and everything should work. > > On Tue, Apr 28, 2015 at 11:47 AM Ryan G > wrote: > >> ok, thanks. Let me look at this. When I look at the information about >> the tool, Galaxy does see the exit code is 0, which I think would be >> sufficient to know the tool ran correctly. >> >> >> On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock >> wrote: >> >>> You probably need to set the tag, since due to a >>> historical design choice by default any output on stderr >>> is treated as an error. See: >>> >>> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax >>> >>> Peter >>> >>> On Tue, Apr 28, 2015 at 4:41 PM, Ryan G >>> wrote: >>> > Hi - I implemented a tool I us into Galaxy but when I run the tool >>> view >>> > Galaxy, Galaxy thinks the tool failed. I checked the output file the >>> tools >>> > create, and it succeeded. >>> > >>> > How do I tell Galaxy that a tool it ran was successful? Is it >>> something in >>> > my XML file? The tool is outputting some info to stderr. Could this >>> be >>> > why? >>> > >>> > ___ >>> > Please keep all replies on the list by using "reply all" >>> > in your mail client. To manage your subscriptions to this >>> > and other Galaxy lists, please use the interface at: >>> > https://lists.galaxyproject.org/ >>> > >>> > To search Galaxy mailing lists use the unified search at: >>> > http://galaxyproject.org/search/mailinglists/ >>> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed
ok, thanks. Let me look at this. When I look at the information about the tool, Galaxy does see the exit code is 0, which I think would be sufficient to know the tool ran correctly. On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock wrote: > You probably need to set the tag, since due to a > historical design choice by default any output on stderr > is treated as an error. See: > > https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax > > Peter > > On Tue, Apr 28, 2015 at 4:41 PM, Ryan G > wrote: > > Hi - I implemented a tool I us into Galaxy but when I run the tool view > > Galaxy, Galaxy thinks the tool failed. I checked the output file the > tools > > create, and it succeeded. > > > > How do I tell Galaxy that a tool it ran was successful? Is it something > in > > my XML file? The tool is outputting some info to stderr. Could this be > > why? > > > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] new tool works correctly but galaxy thinks it failed
Hi - I implemented a tool I us into Galaxy but when I run the tool view Galaxy, Galaxy thinks the tool failed. I checked the output file the tools create, and it succeeded. How do I tell Galaxy that a tool it ran was successful? Is it something in my XML file? The tool is outputting some info to stderr. Could this be why? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Data Libraries
This could work. In the long run though, after sequencing for a project, we'd like them people in the sequencing lab to be able to add the data to Galaxy in project specific libraries, without having an admin create a library for them. On Thu, Apr 23, 2015 at 4:56 PM, Martin Čech wrote: > Hello Ryan, > > it is currently not possible to give users rights to create data > libraries. However you can create the libraries for them and give them > rights to create and manage subfolders (doing the same things but one level > below). > Would that address your goal? > > Martin > > On Thu, Apr 23, 2015 at 4:33 PM Ryan G > wrote: > >> Hi all - We are trying to use Galaxy as a mechanism for our sequencing >> lab to create data libraries for data they generate. I noticed in the >> docs, only Admins are able to create data libraries. Is there a way to >> change this? I'd like to give specific users in our group this ability >> without giving them admin rights. >> >> Ryan >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Data Libraries
Hi all - We are trying to use Galaxy as a mechanism for our sequencing lab to create data libraries for data they generate. I noticed in the docs, only Admins are able to create data libraries. Is there a way to change this? I'd like to give specific users in our group this ability without giving them admin rights. Ryan ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] "This job is waiting to run"
Thank you. its was the job_conf.xml that wasn't set up properly. I have a simply job_conf.xml that works well. sharing for the group: /opt/sge/ge2011.11/lib/linux-x64/libdrmaa.so On Thu, Feb 5, 2015 at 10:03 PM, John Chilton wrote: > Assuming grid engine is working outside of Galaxy and the Galaxy user > can say qsub files just fine - then you need to install the sun grid > engine libdrmaa package - or build from scratch. Assuming you have > done that and the resulting .so file is > /usr/lib/gridengine-drmaa/lib/libdrmaa.so. Then all you should have to > do is create a config/job_conf.xml file in your Galaxy root that looks > something like this: > > > > > load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"> > id="drmaa_library_path">/usr/lib/gridengine-drmaa/lib/libdrmaa.so > > > > > > > > > > > > > > > > A slightly more complicated setup with supervisor, uwsgi, multiple > handlers, etc... all on grid engine is covered in this tutorial that > Nate put together last year > ( > https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay/AdminWalkthrough#Configure_Galaxy > ). > This job_conf.xml is a stripped down version of the one from that > tutorial. > > In terms of rolling back and just getting jobs to start running again > - you need to remove $GALAXY_ROOT/config/job_conf.xml and > $GALAXY_ROOT/job_conf.xml and things should start working using the > local runner again. If this isn't working - there maybe a problem in > your galaxy.ini file - I would need to know what properties were being > set in there to know more though. > > -John > > > On Mon, Feb 2, 2015 at 12:53 PM, Ryan G > wrote: > > I tried setting up Galaxy to use Sun Grid Engine, but failed miserably. > I > > removed my config/job_conf.xml hoping Galaxy would revert to its default > > state, but jobs are no longer being dispatched. I don't see any errors > in > > the log. > > > > How can I get Galaxy to 1) use SGE, or 2) revert to its default state for > > running jobs. The page, > > https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster isn't > 100% > > clear on how to set up a simply configuration for SGE. I'd be happy to > > contribute mine as an example, if I can get it running. > > > > > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tools to download SRA datasets from GEO
Thanks Hans-Rudolf. I didn't see the EBI SRA link before. But not sure what will do what I want. I want to be able to plug in an SRA # and have the tool download the data and prep it for analysis. Right now, it looks like I need to click through the EBI website to get the data. I found a tool in the toolshed but haven't had a chance to look at it. That is my next step. On Thu, Feb 5, 2015 at 3:18 AM, Hans-Rudolf Hotz wrote: > Hi > > Are you looking for any special GEO data, which is not mirrored at the > ENA? If not, you can probaly use the "Get Data" -> "EBI SRA" tool, which > is part of the installation. > > Also, have you looked at the toolshed? e.g. > https://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit > > > Regards, Hans-Rudolf > > > > On 02/04/2015 04:44 PM, Ryan G wrote: > >> Do any tools exist to download GEO datasets from NCBI? >> >> >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >>https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >>http://galaxyproject.org/search/mailinglists/ >> >> ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tools to download SRA datasets from GEO
Do any tools exist to download GEO datasets from NCBI? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] "This job is waiting to run"
I tried setting up Galaxy to use Sun Grid Engine, but failed miserably. I removed my config/job_conf.xml hoping Galaxy would revert to its default state, but jobs are no longer being dispatched. I don't see any errors in the log. How can I get Galaxy to 1) use SGE, or 2) revert to its default state for running jobs. The page, https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster isn't 100% clear on how to set up a simply configuration for SGE. I'd be happy to contribute mine as an example, if I can get it running. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] SGE integration
I'm trying to get my instance of Galaxy working with Sun Grid Engine. The page https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster is not 100% clear on how to do this but I here's what my job_conf.xml looks like: /apps/sys/sge/ge2011.11/lib/linux-x64/libdrmaa.so I tried to submit a job via Galaxy and at first the log files indicated the shell script got created in the job_working_dir and I was a job ID, but when the job completed, Galaxy didn't know about it. Now, I have no jobs runnings and I can't submit anything via Galaxy. It doesn't appear to submit them to SGE or even create the directory for the job. Pastor.log doesn't show anything either. So, I guess I could use a little help with getting Galaxy running with SGE. I have a simple set up so nothing fancy. Any ideas where to get started? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Manually installing rsem_datatypes package from toolshed
Yup, that fixed it. Thanks! On Wed, Jan 21, 2015 at 6:51 PM, John Chilton wrote: > I believe this is an ancient bug that I has been fixed in Galaxy's > central branch but is not in the latest release: > > > https://bitbucket.org/galaxy/galaxy-central/commits/1422966f1ca88472b8685015f5a8cdd3dd0f1db9 > > The previous workaround for this bug was that one would need to import > the datatype at the top of registry.py (import rsem_datatypes) which > is another option for addressing this problem instead of applying the > patch. > > Hope this helps, > -John > > > On Wed, Jan 21, 2015 at 2:16 PM, Ryan G > wrote: > > I'm trying to manually install rsem_datatypes package into my local > Galaxy > > install. I can't use the Toolshed for various reasons. > > > > Anyway, I downloaded the package using > > > > hg clone https://toolshed.g2.bx.psu.edu/repos/jjohnson/rsem_datatypes > > > > I see two files: > > > > 1) datatypes_conf.xml, and > > 2) rsem.py > > > > I copied the lines into my > > config/datatypes_conf.xml file. > > I also copied rsem.py to lib/galaxy/datatypes/. > > > > When I restart Galaxy, it doesn't seem that Galaxy knows how to handle > rsem > > datatypes, as I get this error: > > > > galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing > > datatype module galaxy.datatypes.rsem: 'module' object has no attribute > > 'rsem' > > Traceback (most recent call last): > > File "/data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line > > 210, in load_datatypes > > module = getattr( module, mod ) > > AttributeError: 'module' object has no attribute 'rsem' > > galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing > > datatype module galaxy.datatypes.rsem: 'module' object has no attribute > > 'rsem' > > Traceback (most recent call last): > > File "/data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line > > 210, in load_datatypes > > module = getattr( module, mod ) > > AttributeError: 'module' object has no attribute 'rsem' > > galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,520 Error importing > > datatype module galaxy.datatypes.rsem: 'module' object has no attribute > > 'rsem' > > Traceback (most recent call last): > > File "/data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line > > 210, in load_datatypes > > module = getattr( module, mod ) > > AttributeError: 'module' object has no attribute 'rsem' > > > > I'm obviously missing something but not sure what. I suspect maybe the > > rsem.py file is not in the right place? > > > > Ryan > > > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Manually installing rsem_datatypes package from toolshed
I'm trying to manually install rsem_datatypes package into my local Galaxy install. I can't use the Toolshed for various reasons. Anyway, I downloaded the package using hg clone https://toolshed.g2.bx.psu.edu/repos/jjohnson/rsem_datatypes I see two files: 1) datatypes_conf.xml, and 2) rsem.py I copied the lines into my config/datatypes_conf.xml file. I also copied rsem.py to lib/galaxy/datatypes/. When I restart Galaxy, it doesn't seem that Galaxy knows how to handle rsem datatypes, as I get this error: galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing datatype module galaxy.datatypes.rsem: 'module' object has no attribute 'rsem' Traceback (most recent call last): File "/data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 210, in load_datatypes module = getattr( module, mod ) AttributeError: 'module' object has no attribute 'rsem' galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,519 Error importing datatype module galaxy.datatypes.rsem: 'module' object has no attribute 'rsem' Traceback (most recent call last): File "/data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 210, in load_datatypes module = getattr( module, mod ) AttributeError: 'module' object has no attribute 'rsem' galaxy.datatypes.registry ERROR 2015-01-21 14:01:47,520 Error importing datatype module galaxy.datatypes.rsem: 'module' object has no attribute 'rsem' Traceback (most recent call last): File "/data/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 210, in load_datatypes module = getattr( module, mod ) AttributeError: 'module' object has no attribute 'rsem' I'm obviously missing something but not sure what. I suspect maybe the rsem.py file is not in the right place? Ryan ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Manually adding new tools from toolshed
I can try a local toolshed, but the organization I work at frowns upon automatic installation for various reasons. That and it lets me see exactly how a tool is installed and works within my local instance. When a tool is installed from the toolshed, how does Galaxy know about it? >From a DB entry, or from the XML file(s) being present somewhere? I sort of like the idea of how /etc/profile.d gets scanned by /etc/bashrc when a user logs into a linux machine. This way, there is no modification of files, just placing the right files in the right directory is all that is needed. Anyway, I need to understand how Galaxy works with the toolshed. On Fri, Jan 16, 2015 at 3:08 AM, Björn Grüning wrote: > Hi Ryan, > > what about a local bootstrapped ToolShed which is in sync with the > public one (at least for the users you are interested on). Than you can > install from this ToolShed. I guess this is less annoying than > maintaining everything on your own. > > Cheers, > Bjoern > > Am 16.01.2015 um 08:22 schrieb Peter Cock: > > On Thu, Jan 15, 2015 at 6:57 PM, Ryan G > wrote: > >> Because of the way the infrastructure for my Galaxy instance is set up, > I > >> need to download and install tools from the toolshed manually. For > most of > >> the tools, this is pretty easy, however I'm now trying to add RSEM to my > >> instance and it has some new datatypes. > >> > >> Along with the new data types is python class file. I'm referring to > the > >> exist datatypes_conf.xml.sample but don't see a reference to > datatype_files > >> as is coded in the RSEM tool. > >> > >> So my question is, how can I manually install a tool such as RSEM from > the > >> toolshed? I've cloned it but not sure where to put the files and what > to > >> modify in Galaxy's configuration to see the new files. I can modify the > >> datatypes_conf.xml and include the datatypes, but I get the sense this > is > >> not correct. > >> > >> Ryan > > > > The old pre-ToolShed way to add a new datatype was indeed to > > add it to datatypes_conf.xml and put any Python file into the > > galaxy-dist/lib/galaxy/datatypes/ > > > > I'm still doing this on some of my locally developed tools, but > > now they are in the ToolShed perhaps I should switch to using > > that... > > > > Regards, > > > > Peter > > > > P.S. You also used to need to add an import line to the > > galaxy-dist/lib/galaxy/datatypes/registry.py but that is not > > longer required as of this bug fix: > > > https://bitbucket.org/galaxy/galaxy-central/commits/1422966f1ca88472b8685015f5a8cdd3dd0f1db9 > > ___ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Manually adding new tools from toolshed
Because of the way the infrastructure for my Galaxy instance is set up, I need to download and install tools from the toolshed manually. For most of the tools, this is pretty easy, however I'm now trying to add RSEM to my instance and it has some new datatypes. Along with the new data types is python class file. I'm referring to the exist datatypes_conf.xml.sample but don't see a reference to datatype_files as is coded in the RSEM tool. So my question is, how can I manually install a tool such as RSEM from the toolshed? I've cloned it but not sure where to put the files and what to modify in Galaxy's configuration to see the new files. I can modify the datatypes_conf.xml and include the datatypes, but I get the sense this is not correct. Ryan ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
