Re: [galaxy-dev] advice on a mixed cloud/SGE architecture

and the documentation seems a bit > sparse. So any advice on this is most welcome. > > -Nick > > > > On Tue, May 28, 2013 at 3:58 PM, Dannon Baker wrote: > >> Hi Nick, >> >> Not sure I completely understand what you're trying to do here. So, you >

Re: [galaxy-dev] php script integration query

As long as you're able to execute your php script from the command line, it should work fine. -Dannon On Wed, May 29, 2013 at 7:25 AM, Prasun Dutta wrote: > Hi, > > If I have some programs in php which I need to integrate in Galaxy as a > tool, can I do it? I know if I have some programs writte

Re: [galaxy-dev] Creating multiple datasets in a libset

RBWH) > Sent: Wednesday, 29 May 2013 2:45 PM > To: galaxy-dev@lists.bx.psu.edu; 'Dannon Baker'; 'robert.lecl...@gmail.com > ' > Subject: Re: Creating multiple datasets in a libset > > Hi Guys, > Did you manage to get multiple datasets working? I

Re: [galaxy-dev] finding parts of tool_conf.xml

ff > > Thanks, > VJ. > > On Tue, May 28, 2013 at 12:42 PM, Dannon Baker wrote: > >> I'm assuming you're referring to main.g2.bx.psu.edu's tool configuration >> as a reference. Some of these components are installed via the tool shed, &g

Re: [galaxy-dev] finding parts of tool_conf.xml

I'm assuming you're referring to main.g2.bx.psu.edu's tool configuration as a reference. Some of these components are installed via the tool shed, and others may have been manually added to main and are not included in the base tool_conf.xml.sample. I may be able to point you in the right directi

Re: [galaxy-dev] Workflow refresh

So you have a galaxy window open and as you upload files via the API, new datasets do appear automatically without refreshing the history. These datasets, however, are in the wrong state and don't update? -Dannon On Thu, May 23, 2013 at 12:01 AM, wrote: > Hi, > >I upload files which

Re: [galaxy-dev] advice on a mixed cloud/SGE architecture

Hi Nick, Not sure I completely understand what you're trying to do here. So, you want to have a galaxy head node on AWS that dispatches jobs to a non-AWS private SGE cluster? -Dannon On Thu, May 16, 2013 at 12:18 PM, Nikolay N. wrote: > Hi, > > I was contemplating setting up a galaxy master

Re: [galaxy-dev] very long load times for some shared libraries...

Hey Brad, This a known issue -- data library refactoring is planned that should help alleviate this. You can follow the progress of it at https://trello.com/card/data-library-ui-progressive-display-of-folders/506338ce32ae458f6d15e4b3/56 -Dannon On Fri, May 17, 2013 at 5:43 PM, Langhorst, Bra

Re: [galaxy-dev] maximum recursion depth error

Hi Ann, Are you able to share more of the stack trace, or a method for reproducing this? I'm assuming it's a local instance you're talking about -- what revision are you running, etc? Thanks! -Dannon On Sat, May 18, 2013 at 3:12 PM, Ann Holtz-Morris, M.S. < aholtzmor...@chori.org> wrote: > H

Re: [galaxy-dev] missing new job lock function

Hi Leon, No, this feature was removed at the time of the job handler refactoring. There are plans to reimplement it in a way compatible with the new job management, but no ETA. -Dannon On Tue, May 21, 2013 at 5:35 AM, Leon Mei wrote: > Dear list, > > I recently updated our local Galaxy to ga

Re: [galaxy-dev] Problem changing username

Thomas, Thanks for reporting this. It looks like there was an internal issue with your user data preventing this update, which I think I've fixed. Care to give it another shot? -Dannon On Wed, May 15, 2013 at 2:54 AM, Thomas Haverkamp < t.h.a.haverk...@ibv.uio.no> wrote: > Hi, > I have been

Re: [galaxy-dev] User expiration date

Hi Nikos, No, it's not currently possible to set individual account expiration dates in Galaxy, though you could probably script this. -Dannon On Wed, May 15, 2013 at 7:12 AM, Nikos Sidiropoulos wrote: > Hi > > Is it possible to set an expiration date for specific user accounts? > > Bests, > N

Re: [galaxy-dev] import Workflow from public Galaxy to local instance

On Wed, May 22, 2013 at 3:12 AM, Andreas Kuntzagk < andreas.kuntz...@mdc-berlin.de> wrote: > But how do I get the workflow_id? For example for the workflow > https://main.g2.bx.psu.edu/u/**gm2123/w/cloudmap-unmapped-** > mutant-workflow-no-candidates

Re: [galaxy-dev] Cloudman / galaxyIndicies

Hey Rob, Yes, you should be able to create your own volume and sub it into pd.yaml. Since you want to share this across several instances, and you can't mount an EBS volume to multiple instances, you'll definitely want to use the snapshot method (and so, snap_id is required). -Dannon On Tue, M

Re: [galaxy-dev] Cloudman - missing security rules in wiki page

Hey Joachim, Thanks for pointing out the discrepancy here. I'll be overhauling the wiki in the near future to correspond with a new Cloudman release and will make sure to update this. -Dannon On Thu, May 16, 2013 at 10:01 AM, Joachim Jacob | VIB | < joachim.ja...@vib.be> wrote: > > Hi all, >

Re: [galaxy-dev] location of .loc-files/data tables -- bug or feature?

Hey Christian, This is a bug that surfaced in revision 8333 which should be fixed in 9326:d07c62f0067a, which is available in the most recent galaxy-dist (stable branch). If you'd rather not update right away, we'll have another full-fledged dist release out soon. -Dannon On Tue, May 21, 2013

Re: [galaxy-dev] workflow startup issues

t; > parent: 9320:47ddf167c9f1 tip > Use Galaxy's ErrorMiddleware since Paste's doesn't return > start_response. Fixes downloading tarballs from the Tool Shed when > use_debug = false. > branch: stable > commit: 18 modified, 178 unknown > update: (current) > &g

Re: [galaxy-dev] import Workflow from public Galaxy to local instance

This interaction is pretty clunky right now (I've made a trello card for improving it: https://trello.com/c/eu8XiJLK. Two options right now are: 1) Import (on main) each workflow you want to copy to your local instance, and generate the regular download link for import. (Download or Export in th

Re: [galaxy-dev] workflow startup issues

Geert, This should be fixed in the up-to-date stable branch as far as I know. Can you tell me what 'hg summary' states? -Dannon On Mon, May 20, 2013 at 4:43 PM, Geert Vandeweyer < geert.vandewey...@ua.ac.be> wrote: > Hi, > > After the latest upgrade (april), I'm having issues when starting (b

Re: [galaxy-dev] selecting multiple inputs for workflows not possible anymore

ob > > Rijvisschestraat 120, 9052 Zwijnaarde > Tel: +32 9 244.66.34 > Bioinformatics Training and Services (BITS) > http://www.bits.vib.be > @bitsatvib > > On 05/16/2013 05:01 PM, Dannon Baker wrote: > >> Your instance isn't quite up-to-date enough fo

Re: [galaxy-dev] selecting multiple inputs for workflows not possible anymore

ied, 267 unknown (new branch head) > update: 11 new changesets (update) > [galaxy@galaxy galaxy-dist]$ hg branch > stable > > > Joachim Jacob > > Rijvisschestraat 120, 9052 Zwijnaarde > Tel: +32 9 244.66.34 > Bioinformatics Training and Services (BITS) > http://www.bits.vib

Re: [galaxy-dev] selecting multiple inputs for workflows not possible anymore

I should have read the rest of my email before replying -- so you did update Galaxy for your cloud instance. What exact revision/branch are you running now? There was a brief period when select2 was enabled for the workflow page and it broke things. This should be fixed in -stable (and, of cours

Re: [galaxy-dev] selecting multiple inputs for workflows not possible

This is probably related to the galaxy version currently available by default in the cloud -- it's significantly out of date. We froze updates to the base volume pending a new Cloudman release (that shouldn't be too much longer in development). You should be able to update the galaxy installation

Re: [galaxy-dev] Function for deleting specific datasets from the history

Hi Aris, 1) Not currently, though you can easily delete all hidden datasets in a history at once using the "Delete Hidden Datasets" option in the history menu. 2) This is intentionally not exposed to the user, though as an administrator you could find this information by looking at the dataset in

Re: [galaxy-dev] Embedding a help text in a Workflow?

Hey Peter, You're correct, currently the only top level description field for a workflow is that Annotation/Notes field. While it wouldn't have rich text, is it reasonable to programmatically generate something like what you're suggesting from the combination of the primary Annotation/Notes field

Re: [galaxy-dev] Error with fastqc

Hi Kathryn, It looks like you haven't installed FastQC (or potentially installed it and just haven't made it accessible to Galaxy). You'll need to install FastQC from http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ if you haven't already, and the main fastqc perl script must be executab

Re: [galaxy-dev] migration error

t 11:03 AM, Peter Cock > wrote: > > On Wed, May 8, 2013 at 10:19 PM, Dannon Baker > wrote: > >> > >> Hey Robert, > >> > >> I assume this is sqlite? And, when you say you ran this without any > >> existing database -- was this was a complete

Re: [galaxy-dev] Getting example_watch_folder.py to work...

Hey Neil, A user browsing that history wouldn't automatically get the updates (unless the history was already refreshing for some reason), but they definitely would upon refresh. Glad you got the rest working! -Dannon On Thu, May 9, 2013 at 2:02 AM, wrote: > Hi all, > > I fina

Re: [galaxy-dev] Error in installing Galaxy.

On Thu, May 9, 2013 at 12:21 AM, sridhar srinivasan < sridhar2bioi...@gmail.com> wrote: > and it is working.. but i could'nt connect to the webpage > http://127.0.0.1:8080/ from another system in same network.. > > By default, galaxy will only be serving on 127.0.0.1 (localhost), which is a loopb

Re: [galaxy-dev] migration error

Hey Robert, I assume this is sqlite? And, when you say you ran this without any existing database -- was this was a completely new clone of galaxy, or did you update a prior installation and delete database/universe.sqlite manually before running? -Dannon On Wed, May 8, 2013 at 2:07 PM, Robe

Re: [galaxy-dev] conditions within workflows

Hi Olivia, Currently it's not possible to have conditional job execution in workflows, though this is definitely something we've talked about adding. The conditional toolbox element repository that you found is actually some of John's work on conditionally having tools in the toolbox, not for mak

Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

at 4:31 PM, Iry Witham wrote: > I did add nodes about the same time I setup load balancing so that was > likely the fix. I will definitely set the head node not to run jobs. > > Thanks, > Iry > > From: Dannon Baker > Date: Monday, May 6, 2013 4:19 PM > > To: I

Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

2013 at 4:15 PM, Iry Witham wrote: > I was not clear how the load balancer worked in this instance, but my > goal was to improve performance. I am not sure this was the correct use, > but it seemed to work. > > From: Dannon Baker > Date: Monday, May 6, 2013 4:12 PM

Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

t the health check to: > > Ping: http:80/ > Timeout: 40 seconds > Interval: 60 seconds > Unhealthy threshold: 2 > Healty threshold: 10 > > As far as autoscaling, I am not really interested since I see no real > need at this point. > > Thanks, > > Iry > > F

Re: [galaxy-dev] Usability bug/inconsistency with workflows versus tools

Thanks for the suggestion -- this style should definitely be applied in both places and I've done so in 9659:bcb6e71eda61. -Dannon On Mon, May 6, 2013 at 2:30 PM, Peter Cock wrote: > I seem to be in feedback mode: another little rough edge in Galaxy: > > When using a tool in Galaxy, at the end

Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

orking. > > From: Dannon Baker > Date: Monday, May 6, 2013 3:01 PM > > To: Iry Witham > Cc: "galaxy-dev@lists.bx.psu.edu" > Subject: Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData > partition > > The first thing that comes to mind is a bug that e

Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

> 1000GB. The instance restarted, but the volume remains at 100GB. Is > this due to the lack of disk space? I don't see a snapshot when I look at > the AWS console after the restart. Any ideas? > > Thanks, > > IRy > > From: Dannon Baker > Date: Monday

Re: [galaxy-dev] Resizing galaxy cloudman /mnt/galaxyData partition

Hi Iry, This should work, I use it regularly. Just make sure you're not ssh'ed in and 'in' /mnt/galaxyData or anything like that. There's not really another way to do this that I'd recommend trying if you need the instance to continue working for something tomorrow. Let me know if you have any

Re: [galaxy-dev] workflow multiple inputs

ers, > > Last week we made an update on the default branch of galaxy-dist. > Some problems concerning the api were detected and resolved thanks to > Dannon Baker by pulling the stable branch. > > However, a very interesting fonctionality was working well on this default >

Re: [galaxy-dev] Installing FreeBayes via Toolshed: Tool dependency installation error

ated from the reference and alternate > alleles given the sample ploidy"> > ##FORMAT= Likelihood Explicit, same as GL, but with tags to indicate the specific > genotype. For instance, > 0^-75.22|1^-223.42|0/0^-323.03|1/0^-99.29|1/1^-802.53 represents both > haploid and diploid

Re: [galaxy-dev] Creating multiple datasets in a libset

matted=False) >> if result_ds["state"] == 'ok': >> break >> else: >> time.sleep(1) >> >> >> Rob Leclerc, PhD >> <http://www.linkedin.com/in/robleclerc><https://twitter.com/#!/roblecl

Re: [galaxy-dev] print out workflow execution commands!

scripts at the ~api/ (ie. > Example_watch, workflow_excute) scripts but I do not think these scripts > can create a new history every time they get executed unless I am totally > off.**** > > ** ** > > Regards > > ** ** > > *From:* Dannon Baker [mailto:dannon.ba...@gmail

Re: [galaxy-dev] routing to a cluster or not on a per-tool basis

Hey Dan, Sure, you can configure per-tool job runners. This wiki page ( http://wiki.galaxyproject.org/Admin/Config/Jobs) should get you started, but let me know if you run into any troubl On Tue, Apr 30, 2013 at 4:47 PM, Dan Tenenbaum wrote: > Hi, > > I have some tools that run really quickly

Re: [galaxy-dev] print out workflow execution commands!

s from outside Galaxy env. I guess I have to dig into the > database, but can you tell me what table(s) should I be looking at to find > out that info? > > ** ** > >**** > > ** ** > > *From:* Dannon Baker [mailto:dannon.ba...@gmail.com] > *Sent:* Tuesday,

Re: [galaxy-dev] print out workflow execution commands!

Hi Hak, Yes, you can get all of the information saved for a particular workflow - in the abstract, not a particular workflow execution - by going to 'Download or Export' in the workflow menu, then click "Download to File". This will give you a .ga file which contains the steps in JSON format, whi

Re: [galaxy-dev] Installing FreeBayes via Toolshed: Tool dependency installation error

Looks like you're missing cmake, a dependency for building FreeBayes. If you're able to install that for your system (available in most package managers) you should be good to go. -Dannon On Tue, Apr 30, 2013 at 1:03 PM, Iry Witham wrote: > Hi All, > > I am trying to get Freebayes installed

Re: [galaxy-dev] Galaxy Workflow Input Problem

Hi Amanda, Sorry about the inconvenience. There's a fix for this issue in galaxy-central that will be available the next time main.g2.bx.psu.edu is updated. Until then, if you remove the "input dataset" step from your workflow and allow the tool itself to act as the starting point, it should all

Re: [galaxy-dev] Creating multiple datasets in a libset

ding > of extra files? > > Cheers, > > Rob > > Rob Leclerc, PhD > <http://www.linkedin.com/in/robleclerc><https://twitter.com/#!/robleclerc> > P: (US) +1-(917)-873-3037 > P: (Shanghai) +86-1-(861)-612-5469 > Personal Email: rob.lecl...@aya.yale.edu > > &g

Re: [galaxy-dev] Galaxy API prob with HTTP_REMOTE_USER

fe690 > user:Nate Coraor > date:Mon Apr 08 12:30:08 2013 -0400 > summary: Merged stable. > > > -- > Olivia > > > Le 29/04/13 15:05, Dannon Baker a écrit : > > Olivia, > > There's a fix for this available in galaxy-central, but

Re: [galaxy-dev] Any hint on how to use Galaxy within virtualenv?

Hi Jean-Francois, Were you able to update to the next galaxy-dist and test? This issue should be resolved in 8771:ae446180fd11, which was added just after the distribution you were using previously. -Dannon ___ Please keep all replies on th

Re: [galaxy-dev] Creating multiple datasets in a libset

Hey Rob, That example_watch_folder.py does just submit exactly one at a time, executes the workflow, and then does the next all in separate transactions. If you wanted to upload multiple filepaths at once, you'd just append more to the ''filesystem_paths' field (newline separated paths). -Dannon

Re: [galaxy-dev] Galaxy API prob with HTTP_REMOTE_USER

Olivia, There's a fix for this available in galaxy-central, but I'm surprised you're seeing it in -dist as I thought the problem was introduced after the dist freeze. Can you provide the output of 'hg tip'? -Dannon On Mon, Apr 29, 2013 at 6:53 AM, Olivia Doppelt wrote: > Hello to All, > > I w

Re: [galaxy-dev] Merging files: Error merging filesglobal name 'shutil' is not defined

Hey Peter, Thanks for the contributions, I've committed the changes to -central. You're definitely right about the merge failure not setting the job status to error, and I'm looking into that now. -Dannon On Thu, Apr 25, 2013 at 6:51 AM, Peter Cock wrote: > Hi all, > > While testing a BLAST s

Re: [galaxy-dev] Any hint on how to use Galaxy within virtualenv?

Jean-Francois, Are you running a current revision of Galaxy? This issue should be resolved in recent galaxy releases. -Dannon On Fri, Apr 19, 2013 at 3:47 PM, Jean-Francois Payotte < jean-francois.payo...@dnalandmarks.ca> wrote: > Dear Galaxy mailing list, > > We ran into the same issue descr

Re: [galaxy-dev] about the permission of stdout and stderr

Hi Bingxin, I think this is resolved in changeset 9332:2cfc5c8223ef, which is available in galaxy's stable branch now. -Dannon On Thu, Apr 18, 2013 at 2:26 AM, BingXin Lu wrote: > Hi all, > I updated my galaxy yesterday, after that every time I clicked stdout and > stderr in the history panel

Re: [galaxy-dev] Reports Web Application fails to start (unable to import TracksterConfig)

Hey Lance, I forgot to reply to this email, but galaxy-central commit 9295:b84e39f2b4db (also available in stable) should resolve this issue. -Dannon On Wed, Apr 3, 2013 at 4:07 PM, Lance Parsons wrote: > After upgrading to the latest distribution release (4.1.2013) I can no > longer start the

Re: [galaxy-dev] Bug report and patch for whitespace

Thanks Peter, you're correct -- I've added this in 9460:da5a5077ef1e. On Wed, Apr 17, 2013 at 10:49 AM, Peter Cock wrote: > Hello all, > > I recently tried adding a tag as follows, > > > blastxml_to_top_descr.py --version > > > This kind of white space is tolerated in the tag,

Re: [galaxy-dev] adding datatypes in tool xml

Hey Robert, Yep, it's documented here: http://wiki.galaxyproject.org/ToolShedDatatypesFeatures -Dannon On Wed, Apr 10, 2013 at 5:50 PM, Robert Baertsch wrote: > If I want to add a new datatype during tool installation from the shed, > how define that in the tool.xml? Is this documented anywher

Re: [galaxy-dev] Resubmit a job if the node fails

Related, but not automatic retries in case of node failures -- you can follow the progress of workflow continuation (without rerunning, etc) here: https://trello.com/c/kpARiWl5 ___ Please keep all replies on the list by using "reply all" in y

Re: [galaxy-dev] How to be an admin?

, 2013 at 9:39 AM, Tobias Hohenaur wrote: > I just hit ctrl c in the terminal to stop. Is that enough? > - Original Message - > >> From: Dannon Baker > >> To: Tobias Hohenaur > >> Cc: Peter Cock ,Galaxy Dev < > galaxy-dev@lists.bx.psu.edu> > &g

Re: [galaxy-dev] How to be an admin?

How is it that you're restarting the server? It might be useful to check galaxy's log to see what's going on -- this would be paster.log in your galaxy directory or perhaps the foreground of the terminal you're executing galaxy from. -Dannon On Tue, Apr 9, 2013 at 9:25 AM, Tobias Hohenaur wrote

Re: [galaxy-dev] removing inputs from a pipeline

Philippe, There's not a way to automatically delete intermediate datasets right now, but what you *can* do using workflow outputs is mark them as hidden. An option was recently added to Galaxy to allow the deletion of all hidden datasets in particular history, after which you could purge them all

Re: [galaxy-dev] What is up with the multiple dataset selection for workflows

> Is there a way to turn this feature off? It is worse than not having it at > all if it is implemented like this > Not sure I get what you want to turn off. You could just use the dropdown like normal? Like I mentioned before, I know the current implementation isn't ideal, it's an intermedi

Re: [galaxy-dev] Is there a way to determine if a tool was run from the UI or from a Workflow step?

There isn't a good way to do it right now. If you wanted to take a stab at it, I'd look into adding a 'source' parameter to the job_params dictionary, similar to how Trackster jobs are handled now. If you come up with something that works well, let us know and feel free to submit a pull request w

Re: [galaxy-dev] What is up with the multiple dataset selection for workflows

To filter and select all, just click the select2 box with the dataset list, type to filter the list, and then either press once for the first match or hold enter for more/all. This isn't optimal, but as you'd guessed it's incremental work towards having more control over matching multiple inputs f

Re: [galaxy-dev] Galaxy - FTP Download Problem

Hey Rob, The Cloudman FTP installation (and really, Galaxy's FTP integration in general) is designed only to get files *into* Galaxy, not for downloading. For downloading, you'll want to just use regular HTTP requests. -Dannon On Mon, Mar 25, 2013 at 5:07 PM, Rob Leclerc wrote: > We have a Cl

Re: [galaxy-dev] REST API

Hey Marc, Yep, the '38' in this case is the step id shown just after "steps", but it would be an id listed in that 'inputs' dict. The inputs dictionary should be a list of all the "Input Dataset" steps for the workflow -- yours just doesn't have any and you'll need to add these to be able to map

Re: [galaxy-dev] EBI SRA for local galaxy

Sure! This tool comes with the main galaxy distribution as of '6443:4a39bc209487' (~Jan 2012), you just need to enable it. If you're at or beyond that revision, to enable it you'll just need to add the tool from "data_source/ebi_sra.xml" to your tool_conf.xml if it isn't already there. -Dannon

Re: [galaxy-dev] Setting up Cloudman instance

On Fri, Mar 22, 2013 at 8:40 AM, Iry Witham wrote: > I am working on setting up a Cloudman instance for a course we are > preparing. I have used the link provided: http://usegalaxy.org/cloudlaunch > and can get an instance running. The issues are as follow: > > 1. I need to add tools and have

Re: [galaxy-dev] Cannot update Cloudman from a clean install on EC2?

BUG 2013-03-21 19:46:37,426 Loaded tool data table > 'blastdb' > galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table > 'bowtie_indexes' > galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table > 'bowtie_indexes_color' &g

Re: [galaxy-dev] Cannot update Cloudman from a clean install on EC2?

Hey Brian, Sorry for the delayed response on this one, what you're seeing is a consequence of how Galaxy's tool migration scripts work -- all you should need to do is click restart one more time in the cloudman admin UI. -Dannon On Thu, Mar 14, 2013 at 10:56 PM, Brian Lin wrote: > Hi guys, I'm

Re: [galaxy-dev] What are wrappers, how can I use this?

Sure, tools can be written in anything you'd like -- the wrapper you're referring to is just XML that tells galaxy how to interact with your command line tool. Here are some resources that should get you started: http://screencast.g2.bx.psu.edu/toolIntegration/ http://wiki.galaxyproject.org/Admin

Re: [galaxy-dev] Is parallelism not working with galaxy-central?

Björn, Peter, and John, Thanks for finding and fixing this issue -- the fix has been merged into galaxy-central and should be available with the next distribution release currently scheduled for April 1. We're also looking into adding parallelism tests to our normal testing procedure to prevent t

Re: [galaxy-dev] Count characters in column

Hi Greg, You can do this using the "Compute" tool in the Text Manipulation section. Your expression in this case, to add a column with the number of "A" nucleotides in column 1, would be something like: str(c1).count("A") Thanks for using Galaxy! -Dannon On Fri, Mar 15, 2013 at 5:05 PM, Thysse

Re: [galaxy-dev] Datatype dropdown only 8px wide

The fix for this issue is in revision 0ea9f5196fde, see: https://bitbucket.org/galaxy/galaxy-central/commits/0ea9f5196fde This is not yet available in galaxy-dist, but will be in the near future. -Dannon On Wed, Mar 13, 2013 at 9:05 PM, Nikhil Joshi wrote: > P.S. I am not a galaxy developer :)

Re: [galaxy-dev] example_watch_folder.py : URL did not return JSON data

ot familiar with python, but I can't see where > 'library[0]['id']' is set or is in scope, since this seems to be the item in > the iterator above this section. > > > Cheers, > > Rob > > > > Rob Leclerc, PhD > <http://www.linkedin.com/in/roble

Re: [galaxy-dev] example_watch_folder.py : URL did not return JSON data

The second argument there should point to the url of Galaxy's API -- in this case http://localhost:8080/api, I'm guessing. -Dannon On Tue, Mar 12, 2013 at 6:11 PM, Rob Leclerc wrote: > > I'm trying to get the example_watch_folder.py to work with a simple example, > but I am running into an error

Re: [galaxy-dev] Some problems setting up a new cloudman instance on AWS

; paste.parsed_querystring([('changeset_revisions', '1d2730e6bb39'), > ('repository_ids', '5483924c34f005f2')], > 'changeset_revisions=1d2730e6bb39&repository_ids=5483924c34f005f2') > paste.printdebug_listeners[, > ] > paste.recursiv

Re: [galaxy-dev] BioBlend: Problem Running Example file

Rob, The request below library_create_library looks like it has the wrong url, it should be: ./library_create_library.py 8c25bc83f6f9e4001dd21eb7b64f063f http://localhost:8080/api/libraries api_test 'API Test Library' -Dannon On Fri, Mar 8, 2013 at 11:40 AM, Rob Leclerc wrote: > I'm have the s

Re: [galaxy-dev] Some problems setting up a new cloudman instance on AWS

On Thu, Mar 7, 2013 at 8:21 AM, Adam Cohn wrote: > Hi Galaxy Admin list, > > This is my first post to this list. Galaxy is a great tool and I am > really enjoying working with it. > > Background, I am setting up a private galaxy instance for my company using > AWS. The installation is going ver

Re: [galaxy-dev] no module named gmap

Is this a fresh clone from galaxy-dist or have you pulled it from somewhere else? It looks like your galaxy clone's lib/galaxy/datatypes/registry.py has been altered to have an extra import, 'gmap', for gmap tools. -Dannon On Wed, Mar 6, 2013 at 12:08 PM, David Hoover wrote: > Hi, > > I'm tryin

Re: [galaxy-dev] How to count the number of Workflow steps?

: > Hi Dannon, > Thanks for the response. If there is a "RenameDatasetActionoutput_file" > post job action, does that implicity mean that all other output files are > considered HideDatasetActions? > thanks, > Richard > > On Tue, Mar 5, 2013 at 6:36 PM, Dannon

Re: [galaxy-dev] How to count the number of Workflow steps?

Manually adding "HideDatasetActions" via the right panel in the editor was deprecated a while back in favor of the workflow output 'asterisks' you see rendered on each step in the workflow editor, but they're still used behind the scenes. When you flag a step as an output, all other non-output ste

Re: [galaxy-dev] Authentication: email addresses are not validated prior to account creation

Vipin, I don't know of anyone who's done this, but if anyone wants to take a stab at it, it's definitely something that we could include (as long as it's optional, configurable in universe_wsgi.ini) in Galaxy. -Dannon On Fri, Mar 1, 2013 at 10:39 AM, Vipin TS wrote: > Hello members, > > I beli

Re: [galaxy-dev] Resizing EBS on Amazon

Unfortunately the snapshotting process used by the is really slow, as you've noticed, and there's not much we can do to make that faster. We've discussed other methods for growing the filesystem but haven't finished it yet. For working with S3, instead of s3fs you're more than welcome to give Gal

Re: [galaxy-dev] Error when upgrading the database to version 110

On Mon, Mar 4, 2013 at 7:59 AM, Hans-Rudolf Hotz wrote: > @ Dannon > > > > While we definitely do recommend that if you have the option to > > choose, go with postgres, Galaxy should function both now and in the > > future with MySQL. In this case, your galaxy will function just fine > > without

Re: [galaxy-dev] Composite datatype output for Cuffdiff

Alex, To reiterate what Jeremy has already said on the mailing list, this is definitely something we want, and need, for Galaxy. While this particular implementation has a lot of good parts, creating these collections as first-class composite datasets isn't ideal and we'd be stuck supporting them

Re: [galaxy-dev] [External] Re: data from galaxy

n with either > user. When I added additional user at cloud panel to access galaxy’s admin, > in “manage users” there is no user there. > > ** ** > > Thanks for the help, > > Kathryn > > ** ** > > *From:* Dannon Baker [mailto:dannon.ba...@gmail.com]

Re: [galaxy-dev] Error when upgrading the database to version 110

The problem is that, like you pointed out, mysql allows identifier lengths of 255 for everything except indexes, which are stuck at 64. Most of the index names in Galaxy are auto-generated by SqlAlchemy, the ORM layer we use, based on the names of the tables and columns, and quite a few of these c

Re: [galaxy-dev] [External] Re: data from galaxy

early convenience!! I need > to retrieve them for tomorrow morning meeting. > Kathryn > > -Original Message- > From: Dannon Baker [mailto:dannonba...@me.com] > Sent: Monday, January 21, 2013 9:51 AM > To: Sun, Wenping [USA] > Subject: Re: [External] Re: data from galax

Re: [galaxy-dev] Problem with Upload File tool via url

ur public > server and there was an interference. > > God bless you! I really appreciate your help!! > > > Kind regards, > Zinon > > > On 1/3/2013 3:37 μμ, Dannon Baker wrote: > > Oh, *your* public server! I misread that completely in your first email, > sorry.

Re: [galaxy-dev] [External] Re: macs error for chipseq data

n On Wed, Feb 27, 2013 at 6:34 PM, Sun, Wenping [USA] wrote: > Hello, > When I sudo galaxy user at ssh terminal, the password prompted for galaxy. > What is it? > Thanks, > Kathryn > > -Original Message- > From: Dannon Baker [mailto:dannonba...@me.com] > Sent: F

Re: [galaxy-dev] Problem with Upload File tool via url

My hunch is that the source location is probably responding with an error page and not the actual content you're looking for. Is the source URL behind any authentication scheme, and can you verify that from, say, curl or wget that it works and responds with the data? -Dannon On Fri, Mar 1, 2013

Re: [galaxy-dev] Problem with saving workflows

Hi Alex, Could you open the javascript console in your browser and tell me what, if any, errors you see when you try to save? -Dannon On Thu, Feb 21, 2013 at 5:48 AM, Alexander Kurze wrote: > Hello, > > I am running a local server of Galaxy. I have a problem with editing and > then saving alre

Re: [galaxy-dev] [galaxy-user] Installing new tools from the tool shed

s the > Galaxy in Bio-Linux screwed up? > > Many thanks, > > DJ > > > 2013/2/13 David Joly >> >> This could be the problem, I just installed BioLinux 7 on my computer with >> Galaxy running out-of-the-box... >> >> However, it looks like they changed

Re: [galaxy-dev] galaxy-dev mailing list

Hi Oya, Here's a wiki page detailing how to subscribe and unsubscribe from any of the galaxy mailing lists: -Dannon 2013/2/14 Oya Uyguner : > I would like to enroll, galaxy-dev mailing list. > Regards, > Z. Oya Uyguner > Department of Medical Genetics > Istanbul Medical Faculty > Istanbul Univer

Re: [galaxy-dev] can't run instance for CloudMan

Stefano, Could you clarify what you did differently? The public URL provided by Amazon *should* be the primary interface to your cluster. -Dannon On Tue, Feb 19, 2013 at 12:55 PM, stefano cardinale wrote: > Hello, > thanks, I managed to run the instances by using BioCloudCentral on the same

Re: [galaxy-dev] shall we need to download dataset when we install our local Galaxy?

Hi! You'll probably find this page helpful in configuring your local instance with tools and references: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup In short, yes, to use these references locally you'll need to retrieve them and configure your galaxy to use them. -Dannon On Mon, Fe

Re: [galaxy-dev] Merge internal head to release_2012.02.08

Derrick, The new update process outlined works with local changes the same way as the 'hg pull -u' used previously. The only difference is that it updates to a particular tag, instead of whatever is at the galaxy-dist tip. 'hg pull -u' that you've used before is actually just shorthand for doing

Re: [galaxy-dev] New release : display problem

To answer to Carlos, I have the problem with Firefox and Chrome. > > Cheers, > Mathieu > > - Mail original - >> De: "Dannon Baker" >> À: "Mathieu Bahin" >> Cc: galaxy-dev@lists.bx.psu.edu >> Envoyé: Jeudi 14 Février 2013 17:01:02 >

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