Re: [galaxy-dev] [galaxy-iuc] Test ToolShed package_samtools_0_1_19 status error?

Peter, Based on the latest test run, and my own investigations, it would appear that the samtools compilation process is looking in the wrong include path for ncurses/ncurses_dll.h. My recommendation would be to replace the following: -I$NCURSES_INCLUDE_PATH/ncurses/ with -I$NCURSES_INCLUD

Re: [galaxy-dev] Galaxy Error Message

So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R '/Users/bbelfio1/Documents/sample.txt' '04110' 'HSA' Error in grep(species, pathway.id) : argument "pathway.id" is missing, with no default Calls: pathview -> gre

Re: [galaxy-dev] Galaxy Error Message

Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R Error in value[[3L]](cond) : failed to read experimental design data: cannot open the connection Calls: tryCatch -> tryCatchList -> tryCatchOne -> In addition: W

Re: [galaxy-dev] Galaxy Error Message

The initial error now seems to be taken care of and now am getting this message on attempting to run tool: File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 153, in prepare_job job_wrapper.runner_command_line = self.build_command_line( job_wrapper, include_metadata=i

Re: [galaxy-dev] [galaxy-iuc] Test ToolShed package_samtools_0_1_19 status error?

Hi Dave, This problem persists (or has reoccured), This tool dependency's required tool dependency samtools version 0.1.19 has status Error. Did you discover anymore last week? Sorry for the lag in my reply, I busy with other things. Thanks, Peter On Mon, Apr 21, 2014 at 2:24 PM, Dave Bouvier

Re: [galaxy-dev] Galaxy Error Message

Hi Brad On 04/28/2014 05:26 PM, Bradley Belfiore wrote: So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R '/Users/bbelfio1/Documents/sample.txt' '04110' 'HSA' I said "Rscript_wrapper.sh /Users/bbelfio1/galaxy-

Re: [galaxy-dev] Galaxy Error Message

This is not what I suggested, I said Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output replacing $genedata $pathwayid $species $output with meaningful arguments On 04/28/2014 04:29 PM, Bradley Belfiore wrote: Yes when running in

Re: [galaxy-dev] Galaxy Error Message

> On 04/28/2014 03:58 PM, Bradley Belfiore wrote: >> >> The initial error now seems to be taken care of and now am getting this >> message on attempting to run tool: >> >> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", >> line 153, in prepare_job >> job_wrapper.runner_

Re: [galaxy-dev] Galaxy Error Message

again, have you tried running your Rscript outside of Galaxy called by Rscript_wrapper.sh ? To me, it looks like you have a bug in your Rscript and/or your wrapper. Hans-Rudolf On 04/28/2014 03:58 PM, Bradley Belfiore wrote: The initial error now seems to be taken care of and now am getting

Re: [galaxy-dev] Galaxy Error Message

On Mon, Apr 28, 2014 at 2:40 PM, Hans-Rudolf Hotz wrote: > On 04/28/2014 03:32 PM, Bradley Belfiore wrote: >> >> Thank you for your quick response, my command tag is: >> >> interpreter="bash">Rscript_wrapper.sh >> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata >> $pathwayid $spec

Re: [galaxy-dev] Galaxy Error Message

"Please keep all replies on the list by using "reply all"" well, what happens if you run Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output on the command line yourself (or rather as the user galaxy is running as), replacing $gened

Re: [galaxy-dev] Galaxy Error Message

Hi Brad I don't you are using R to execute your R script How do you call your R script, ie how does the command tag looks in the tool definition file? Also, why do you have a "#!/bin/bash" at the beginning of your R script? Regards, Hans-Rudolf On 04/27/2014 09:50 PM, Bradley Belfior

[galaxy-dev] Galaxy Error Message

I am new to galaxy and while trying to convert an R tool to a Galaxy usable tool I keep getting: /Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1: syntax error near unexpected token `(' /Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1: `args=(commandArgs(TRUE))' any h

Re: [galaxy-dev] Galaxy - Cloudman

Hey Dannon, I am using Galaxy (Cloudman) to analyze RNA seq data. I have a bunch of datasets that I ran TopHat on. I am now trying to run Cufflinks etc. I used the same data and workflow yesterday to run Cufflinks etc and that worked fine. I used my own reference annotation (Homo sapiens hg38)

Re: [galaxy-dev] Galaxy/Cloudman Compute Nodes User

Actually, both of these help. I'm putting a boto.conf file into /mnt/galaxy/galaxy-app and setting the BOTO_PATH environment variable from the python script that needs it, so it will work in dev (non-clusterman setup) and production. Jim On Fri, Apr 25, 2014 at 11:20 AM, Dannon Baker wrote: > A

Re: [galaxy-dev] Galaxy/Cloudman Compute Nodes User

Ahh, sorry about that, I misread the bit about it actually needing to be in the user's directory. You could use a worker_post_start_script to configure things like this (creating/copying .boto at boot from the shared space in the script). See https://wiki.galaxyproject.org/CloudMan/UserDatafor ho

Re: [galaxy-dev] Galaxy/Cloudman Compute Nodes User

Hi Jim, /mnt/galaxy is shared via NFS with all cluster workers -- this (or a subdirectory) should work for you. -Dannon On Fri, Apr 25, 2014 at 10:56 AM, Jim McCusker wrote: > Hi all, > > I need to add a .boto file to the user that galaxy jobs get exec'ed as on > cloudman nodes. I thought it w

[galaxy-dev] Galaxy/Cloudman Compute Nodes User

Hi all, I need to add a .boto file to the user that galaxy jobs get exec'ed as on cloudman nodes. I thought it would copy over what the galaxy server has in its home directory, but that doesn't seem to happen. How can I get things like my .boto file to migrate over to new cloudman nodes when they

Re: [galaxy-dev] Galaxy - Cloudman

Do you have Cloudman admin access on this instance? The first thing I'd check would be http:///cloud to verify that your instance has free disk space and to look for any errors in the log. Then, check out the admin service list (http:///cloud/admin) to see if there are any service issues. Next t

Re: [galaxy-dev] Galaxy - Cloudman

Hey Alessia, I'd love to help, but I need a little more context here. Where are you seeing this error, what exactly are you doing when it appears, and can you tell me a little bit more about the Galaxy configuration you're working with? -Dannon On Thu, Apr 24, 2014 at 8:37 PM, Jennifer Jackson

[galaxy-dev] Galaxy - Cloudman

Posting to the galaxy-...@bx.psu.edu mailing list. https://wiki.galaxyproject.org/MailingLists My instance of Galaxy seems to be stuck (same place since last night) and I have received the error message several times now. Pasting the error message below: *Details* user username

Re: [galaxy-dev] [galaxy-iuc] Test ToolShed package_samtools_0_1_19 status error?

The two options I normally use for that are the "Repository dependency definitions" and "Tool dependency definitions" links under the "Valid Galaxy Utilities" heading in the left panel, which provide an overview of all dependencies of the relevant type. --Dave B. On Mon 21 Apr 2014 09:39:51

Re: [galaxy-dev] [galaxy-iuc] Test ToolShed package_samtools_0_1_19 status error?

Thanks Dave, On a slight tangent, is there a way in the ToolShed to see what other repositories use a given repository as a dependency? e.g. From http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19 it there any way to see what uses samtools 0.1.19? Cheers, Peter On Mon, Apr 21,

Re: [galaxy-dev] [galaxy-iuc] Test ToolShed package_samtools_0_1_19 status error?

Peter, From what I've been able to determine, samtools' failure was due to an error in the testing environment startup process, which in turn caused errors in a number of tool dependency packages. I've fixed the initial error, and the next test run should result in a successful samtools insta

[galaxy-dev] Galaxy Hackathon at GCC2014

Galaxy has a fantastic developer community, from the very active mailing lists and #galaxyproject IRC channel to individuals who have submitted literally hundreds of pull requests and patches. We are always looking for ways to interact with existing community members and get even more people invol

Re: [galaxy-dev] galaxy-dev Digest, Vol 94, Issue 22

On Wed, Apr 16, 2014 at 12:16 PM, Dooley, Damion wrote: > Thanks for your input, John. I see, so from what you say, anything installed > via pip in the virtual environment then exists in the module/class include > namespace within galaxy python command line tool code. Good to know. > > I'll no

Re: [galaxy-dev] galaxy-dev Digest, Vol 94, Issue 22

Thanks for your input, John. I see, so from what you say, anything installed via pip in the virtual environment then exists in the module/class include namespace within galaxy python command line tool code. Good to know. I'll note that this approach is compatible with toolshed tools (I'm testi

Re: [galaxy-dev] Galaxy stable not working on MAC OSX, but default is OK

This problem has already been reported and solved. http://user.list.galaxyproject.org/Problem-using-Galaxy-td4648052.html Bernardo 2014-04-12 12:50 GMT+02:00 Bernardo Bello : > Hi, > > Seems I have some problems to run Galaxy stable. Here is the output I > receive when running run.sh. > > Than

Re: [galaxy-dev] [galaxy-user] Trackster error on dbkeys

Hi Jeremy, Thanks for pointing it out. It was indeed an extra line at end of file that caused the problem. It works fine now. I think for organism not found in UCSC, best solution is to upload the genome fasta file and go for edit attributes -> convert FASTA to 2bit and len file . Thanks RT

[galaxy-dev] Galaxy stable not working on MAC OSX, but default is OK

Hi, Seems I have some problems to run Galaxy stable. Here is the output I receive when running run.sh. Thanks for your help, Bernardo -- ---

Re: [galaxy-dev] [galaxy-user] Trackster error on dbkeys

(Moved to galaxy-dev mailing list because it concerns server admin rather than Galaxy usage.) If everything worked fine with a human build but not for PF3d7, then my guess is that the len file for PF3d7 isn’t correctly formatted. Right now, the file parser is very unforgiving—no extra spaces or

Re: [galaxy-dev] Galaxy packages for Bio-Linux - an update + Apache proxying

Hi Tim, I agree the single tool_data_table_conf.xml is a problem and it would be nice to implement functionality for multiple. I've added a Trello card for it here: https://trello.com/c/rm2p8PpZ As to the location file collections, I can foresee a few problems, e.g. conflicting definitions, bad f

Re: [galaxy-dev] Galaxy unhandled exception checking jobs error

Hi John, Thank you so much for this detailed explanation. Before I saw your email I went ahead and manually made changes in the pbs.py script. I didn't follow your mercurial commands and hope that is not a problem down the road (I guess I could use the hg revert option then).This seemed to have

Re: [galaxy-dev] [galaxy-bugs] Galaxy modules deployment

Hello, it is great you want to share tools with others through Galaxy, thank you! We call added software a 'Galaxy tool'. You can start by reading the tool basics in this page: https://wiki.galaxyproject.org/Admin/Tools and then you can browse through wiki where the vast of information about tool

Re: [galaxy-dev] Galaxy unhandled exception checking jobs error

This change is very small and was not committed to the stable branch of galaxy-central so I would just modify the your Galaxy's copy of the pbs runner file directly until the next release: % wget https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c155fa04aa607ff2fec283634df2fb0/raw -O /

Re: [galaxy-dev] Galaxy unhandled exception checking jobs error

John, Thanks for this. I am new to managing galaxy, but how do I go about updating my galaxy to reflect these changes? I found directions on https://wiki.galaxyproject.org/Admin/GetGalaxy#Keep_your_code_up_to_date about pulling changes from the bitbucket repository. Does this preserve my previou

Re: [galaxy-dev] Galaxy unhandled exception checking jobs error

This looks very to similar to an issue discussed here: http://dev.list.galaxyproject.org/pbs-runner-deserializes-server-names-as-unicode-tt4663616.html. The default branch of Galaxy contains changeset that should address this issue - https://bitbucket.org/galaxy/galaxy-central/commits/af5577a24c1

[galaxy-dev] Galaxy unhandled exception checking jobs error

Hi guys, I keep getting an error everytime I start up the galaxy server. I am guessing this has to do with a job that galaxy is trying to resume and cannot find. galaxy.jobs.runners ERROR 2014-04-02 09:31:10,889 Unhandled exception checking active jobs Traceback (most recent call last): File

Re: [galaxy-dev] Galaxy packages for Bio-Linux - an update + Apache proxying

Hi Nate, It's great to hear that my rearrangements for packaging Galaxy are somewhat in line with what you are doing. My package is a bit of a rats-nest of symlinks right now but I'll clean these up as things become more configurable. One thing I'm a bit stuck on is the tool_data_table_conf.xml

Re: [galaxy-dev] Galaxy packages for Bio-Linux - an update + Apache proxying

Hi Tim, I have recently been working on getting Galaxy Main's configs and server-modified files and directories out of the galaxy-dist directory, so our goals are aligning. Not everything can be moved without some trickery (e.g. symlinks) but most paths, including the paths to shed_*.xml are confi

Re: [galaxy-dev] Galaxy startup takes very long. Normal?

I'm using galxy-dist. That's why I don't have the setting. Thanks for the information, I'll wait for the next stable release and update the settings then. Geert On 03/26/2014 01:59 PM, Greg Von Kuster wrote: The changeset that made this a configurable setting was committed to the stable branc

Re: [galaxy-dev] Galaxy startup takes very long. Normal?

The changeset that made this a configurable setting was committed to the stable branch in d270d3c, which was committed on 2014-02-19 https://bitbucket.org/galaxy/galaxy-central/commits/d270d3cf7627a42b6fac2aa69701deadb89c8ffc If you are tracking the stable branch in the galaxy central repo (whic

Re: [galaxy-dev] Galaxy startup takes very long. Normal?

Hi Greg, The setting was not in my universe_sample file. I added it, set log_info to DEBUG and restarted galaxy. The startup time remained the same, and there were many entries in the log file indicating that the lag is indeed the creation of the dependency system: tool_shed.galaxy_instal

Re: [galaxy-dev] Galaxy startup takes very long. Normal?

Hi Geert, The setting should be in your universe_wsgi.ini.sample, and you woud have to manually edit your universe_wsgi.ini to add it. I would say that 125 installed packages is probably what is causing the slow starts. This feature is not currently useful, so it can be set to not function wi

Re: [galaxy-dev] Galaxy startup takes very long. Normal?

hi Greg, I don't have that setting in my universe. Should I just add it? The output of hg summary is (hg incoming doesn't show any available updates): parent: 12276:dc067a95261d tip Added tag release_2014.02.10 for changeset 5e605ed6069f branch: stable commit: 22 modified, 1 deleted, 127 unkn

Re: [galaxy-dev] Galaxy startup takes very long. Normal?

Hello Geert, Do you have a lot of repositories installed from the Tool Shed into you Galaxy instance? if so, the time you're experience may be due to loading the in-memory installed repository registry. Using this registry is optional, but the default configuration setting is to use it. You

[galaxy-dev] Galaxy startup takes very long. Normal?

Dear all, I'm wondering if the following behaviour is normal. Since I reinstalled the latest galaxy distribution, every restart hangs/loads for up to 10 minutes at the following lines: galaxy.model.migrate.check INFO 2014-03-25 15:56:57,965 At database version 118 tool_shed.galaxy_install.m

Re: [galaxy-dev] Galaxy packages for Bio-Linux - an update + Apache proxying

Hi, This is mainly a message to Carlos and Eric who volunteered to get involved with my Debian packaging, but of course any other help will also be appreciated. If either of you can spare time now it is a good moment to do so. I've been working on my package stuff over the last couple of weeks a

Re: [galaxy-dev] Galaxy database size and location

I figured it out. There is an option in the universe.wsgi.ini file called file_path which points to database/file now and can be changed to a diff location. Thanks On Mar 6, 2014, at 1:04 AM, Hans-Rudolf Hotz wrote: > Hi Ravi > > I don't quite understand question. It looks like you are mixing

Re: [galaxy-dev] Galaxy database size and location

I figured it out. There is an option in the universe.wsgi.ini file called file_path which points to database/file now and can be changed to a diff location. Thanks On Mar 6, 2014, at 1:04 AM, Hans-Rudolf Hotz wrote: > Hi Ravi > > I don't quite understand question. It looks like you are mixing

Re: [galaxy-dev] Galaxy reports

ronment before printing this email.* > > > > *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto: > galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Martin Cech > *Sent:* Friday, 7 March 2014 9:09 AM > *To:* Philippe Moncuquet > *Cc:* > *Subject:* Re: [galaxy-dev] Gal

Re: [galaxy-dev] Galaxy reports

eption or interference. Please consider the environment before printing this email. From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Martin Cech Sent: Friday, 7 March 2014 9:09 AM To: Philippe Moncuquet Cc: Subject: Re: [galaxy-dev] Galaxy r

Re: [galaxy-dev] Galaxy reports

Hi Martin, [image: Images intégrées 1] Cheers, Philip 2014-03-07 9:08 GMT+11:00 Martin Čech : > Hello Philip, > > the page you are talking about should look like this: > https://www.dropbox.com/s/r97zvgl8a5h1u4z/Screenshot%202014-03-06%2017.07.52.png > > How does yours look like? > > Martin >

Re: [galaxy-dev] Galaxy reports

Hello Philip, the page you are talking about should look like this: https://www.dropbox.com/s/r97zvgl8a5h1u4z/Screenshot%202014-03-06%2017.07.52.png How does yours look like? Martin On Thu, Mar 6, 2014 at 4:43 PM, Philippe Moncuquet wrote: > Hi, > > We have recently updated our instance, I ha

[galaxy-dev] Galaxy reports

Hi, We have recently updated our instance, I have noticed a bug display in the report page. In the section 'Jobs per Month', the month column does not contain any month name but number instead. Has anybody experienced the same thing ? Regards, Philip __

Re: [galaxy-dev] Galaxy database size and location

Hi Ravi I don't quite understand question. It looks like you are mixing up two different things? A few comments, which might clarify and help you: - the postgresql db does not store the data. It tracks the users, their jobs and their histories. Hence, it stays pretty small. - the actual

[galaxy-dev] Galaxy database size and location

Hi fellow galaxy devs, I am trying to understand how to implement the galaxy database and get an idea of how big it could get. Currently we are running galaxy on a webserver, and want to have the postgresql db on locally mounted partition and not on an NFS partition. This limits us to around 10

[galaxy-dev] Galaxy hack-a-thon at Michigan State HPCC

Hi Galaxy devs, We're deploying Galaxy on the Michigan State HPCC and doing it as a hack-a-thon today. Our authentication is Shibboleth and our scheduler is Torque/Moab, and we're setting it up with 'run as user' with a shared file space /mnt/research/galaxy To set up we've installed base ima

Re: [galaxy-dev] Galaxy command line API information

Hello Benoît, I remember seeing projects trying to do something similar (store workflows internally and execute on Galaxy), like http://refinery-platform.org/, so it could be useful to take a look there too. I've been trying to do something similar but with the Java interface to the Galaxy API ht

Re: [galaxy-dev] Galaxy command line API information

Dear Benoît Meilhac, In my plugin, I would have to import the workflow, then run it with inputs > listed in the executable command line, and after a successful execution, I > would have to retrieve the outputs generated, then delete the created > workflow and any files related that exist. The in

Re: [galaxy-dev] [galaxy-user] Galaxy + user program unable to locate files

Respected Sir, I don't think so that problem is in tool, because when I run same tool of normal terminal, it generate output. What I am thinking is: Consider Galaxy is running from its own directory, my files are in */home/user/Documents/* While uploading file, I am choosing for "Link to files w

[galaxy-dev] Galaxy command line API information

Dear Sir or Madam, I am working for the University of Westminster on the ER-Flow project (http://www.erflow.eu/home). I'm currently investigating a way to use the galaxy workflow engine with a command line interface in order to support it within our project. The idea would be to develop a plugi

Re: [galaxy-dev] [galaxy-user] Galaxy + user program unable to locate files

On Thu, Feb 27, 2014 at 4:20 PM, do kadya wrote: > > I don't think so that problem is in tool, because when I run same tool of > normal terminal, it generate output. This is why I was asking about Perl environment variables - they may be different compared to when you run the tool. For example, i

Re: [galaxy-dev] [galaxy-user] Galaxy + user program unable to locate files

On Thu, Feb 27, 2014 at 9:32 AM, do kadya wrote: > Hi, > Thank You for your kind reply. > > I am having problem in running command in Galaxy. > my current command: > > > > > /usr/bin/x_tool fileList.tab file1.bam file2.bam > > I have created xml file so that i can run this command thr

Re: [galaxy-dev] Galaxy-LIMS and multiple sample

Hello Davide, yes it does. Also these two modifications of Galaxy might be if an interest to you as they enhanced the sample tracking further: http://bcbio.wordpress.com/2011/01/11/next-generation-sequencing-information-management-and-analysis-system-for-galaxy/ http://bioinformatics.oxfordjour

[galaxy-dev] Galaxy-LIMS and multiple sample

Dear all, I don't have an instance of galaxy that manages sequencing requests. I would like to, but I would like to know a single thing: Is the interface friendly enough to make me define multiple sample at once in a single request? Thanks d ___

[galaxy-dev] Galaxy-LIMS and multiple sample

Dear all, I don't have an instance of galaxy that manages sequencing requests. I would like to, but I would like to know a single thing: Is the interface friendly enough to make me define multiple sample at once in a single request? Thanks d ___

Re: [galaxy-dev] Galaxy Tool Shed packages for Biopython

Thanks Peter! +1 for including that into the Biopython release process Cheers, Bjoern On Fri, Sep 13, 2013 at 9:54 AM, Peter Cock wrote: Hi all, I've sent this to both the Galaxy and Biopython developers lists, and hope this will make sense to both groups. If you've not heard of Galaxy, sta

Re: [galaxy-dev] Galaxy Tool Shed packages for Biopython

On Fri, Sep 13, 2013 at 9:54 AM, Peter Cock wrote: > Hi all, > > I've sent this to both the Galaxy and Biopython developers lists, > and hope this will make sense to both groups. If you've not heard > of Galaxy, start here: http://galaxyproject.org - while the easy to > guess Biopython website is

Re: [galaxy-dev] [galaxy-iuc] WARNING:galaxy.datatypes.registry:Overriding conflicting datatype

On Thu, Feb 13, 2014 at 4:22 PM, Greg Von Kuster wrote: > Hi JJ, > > On Feb 13, 2014, at 11:00 AM, Jim Johnson wrote: > >> I now have 2 versions of snpeff installed from the toolshed on my galaxy >> server. >> Each snpeff version includes an identical datatypes_conf.xml >> The galaxy server is s

Re: [galaxy-dev] Galaxy server user activity

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 See https://wiki.galaxyproject.org/Admin/UsageReports On 02/07/2014 02:11 PM, Fenglou Mao wrote: > Dear All, > > We installed a galaxy server here locally, is there any way to generate > a report of the user activity? > > Thanks, > Fenglou > > > _

[galaxy-dev] Galaxy server user activity

Dear All, We installed a galaxy server here locally, is there any way to generate a report of the user activity? Thanks, Fenglou ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions

Re: [galaxy-dev] Galaxy in there server

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 http://getgalaxy.org/ On 02/06/2014 12:11 PM, Bishwo Adhikari wrote: > Hi Galaxy Team, > > I want to install a local instance of Galaxy on our lab server. It is a Unix server with pretty good RAM and storage. > > Is there any wiki page or instruction

Re: [galaxy-dev] Galaxy in there server

On 06/02/2014 19:11, Bishwo Adhikari wrote: Hi Galaxy Team, I want to install a local instance of Galaxy on our lab server. It is a Unix server with pretty good RAM and storage. Is there any wiki page or instruction for installation. Thanks, Bishwo

[galaxy-dev] Galaxy in there server

Hi Galaxy Team, I want to install a local instance of Galaxy on our lab server. It is a Unix server with pretty good RAM and storage. Is there any wiki page or instruction for installation. Thanks, Bishwo ___ Please keep all replie

[galaxy-dev] Galaxy local toolshed - issue hg pushing

Devs, I'm having issues with a local toolshed I'm playing around with. I turned on use_remote = True (since we have that working on our primary galaxy instance). Web access to the tool shed, cloning, and pulling work fine. However, I'm getting "abort: authorization failed" when trying to "hg push

[galaxy-dev] Galaxy problem with DRMAA

Hi everybody, I managed to configure Galaxy to work with DRMAA in our cluster but after the job finished, the dataset state is set to error. Here is the last few lines of the paster.log file: galaxy.jobs.runners.drmaa DEBUG 2014-01-27 10:52:50,449 (181) submitting with credentials: jing [uid:

[galaxy-dev] galaxy tries to access toolshed at http instead of using https

dear all, When I try to install a tool from our local toolshed Galaxy changes the repository url from HTTPS to HTTP and throws an error. I'm setting up a local (intranet) toolshed for some of our in house tools. We run galaxy (latest stable) on HTTPS://nioo0025.nioo.int/galaxy The toolshed is se

Re: [galaxy-dev] [galaxy-user] error:ordinary output of macs in stderr

Hi Han, you can filter the output of every tool and react on it with the stdio tag in Galaxy. for more information please have a look at the wiki page: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cstdio.3E.2C_.3Cregex.3E.2C_and_.3Cexit_code.3E_tag_sets Cheers, Bjoern > Hello,

Re: [galaxy-dev] Galaxy Reports

Thank you Eric for the wiki page. I agree that Galaxy Reports are not visible enough and this might help. Martin, Galaxy Team On Fri, Jan 17, 2014 at 12:29 PM, Eric Rasche wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Well! This is the first I've heard of a Galaxy Reports page.

[galaxy-dev] Galaxy Australasia Workshop (GAW 2014), 24-25 March, Melbourne

Hello all, *We are pleased to announce the 1st Galaxy Australasia Workshop 2014 (GAW 2014) will be held in Melbourne, Australia on 24 and 25th March 2014.* The Galaxy Australasia Workshop is a great op

Re: [galaxy-dev] Galaxy Reports

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Well! This is the first I've heard of a Galaxy Reports page. Too bad I already re-invented the wheel because I hadn't ever heard of this tool... Anyway, since "run_reports.sh" was only mentioned once anywhere in the wiki (according to search, in a Dev

Re: [galaxy-dev] Galaxy Reports link - registed users per month - does not work

Hi Liisa This rings a bell I assume you use a MYSQL database? and I guess other pages are broken as well? We are also using MySQL and I had to fix several lines in several files in order to get all report pages to work. To do the fixes, have a look at this old (but still valid) e-mail

[galaxy-dev] Galaxy Reports link - registed users per month - does not work

Hello, First..I love the Galaxy Reports tool...thanks so much for this. I did however come across an error when trying to few the Registered Users per month link. It would be really nice to have this working :) Thanks in advance, Liisa URL: http://domain:9001/users/registered_users_per_month M

Re: [galaxy-dev] galaxy prod installation with apache proxy

Hey Fernandez, The proxy configuration can be tricky to configure when setting up external display applications, xsendfile (https://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy), etc The problem is that Apache and Galaxy need to access all of the same files and directories. I suspect m

Re: [galaxy-dev] Galaxy packages for Bio-Linux - an update + Apache proxying

Hi John and Carlos, Thanks for your replies regarding my DEB packaging work. Some quick answers to questions you raised. > > In response to the eggs comment in the changelog - there are upsides > and downsides to the way Galaxy handles dependency fetching but I > think there should at least be a

Re: [galaxy-dev] Galaxy packages for Bio-Linux - an update + Apache proxying

Hi Tim, This sounds great. I'll be happy to help testing and hopefully find some time to help packaging once it gets into Debian Med(are you submitting all your packages there?). One question, for apache/nginx configuration why not use something ala phpMyAdmin which ask you if you want to preconf

Re: [galaxy-dev] galaxy local installation

he to take care of the website Cordialement / Regards, Edgar Fernandez De : Carl Eberhard [mailto:carlfeberh...@gmail.com] Envoyé : December-12-13 5:25 PM À : fernandez Edgar Cc : Alistair Chilcott; galaxy-...@bx.psu.edu Objet : Re: [galaxy-dev] galaxy local installation Hello, Edgar - thank

Re: [galaxy-dev] Galaxy packages for Bio-Linux - an update + Apache proxying

This is quite awesome! Thanks for all the hard work Tim. In response to the eggs comment in the changelog - there are upsides and downsides to the way Galaxy handles dependency fetching but I think there should at least be an off switch. I thought that would be easy, but it sounds like not: >From

[galaxy-dev] Galaxy packages for Bio-Linux - an update + Apache proxying

Hi All, As previously mentioned, I'm back working on packaging the Galaxy server as DEB packages for Bio-Linux (ie. Ubuntu 12.04 LTS) and ultimately pushing towards something that could be Debian compliant. There's a way to go in that regard, but I do now have an updated package for Bio-Linux in

Re: [galaxy-dev] galaxy local installation

m Ubuntu to SUSE was occasionally problematic. > > > > Hope this helps. > > > > Regards, > > > > *Alistair * > > > > > > > > *From:* galaxy-dev-boun...@lists.bx.psu.edu [ > mailto:galaxy-dev-boun...@lists.bx.psu.edu] > *On Behalf Of *

Re: [galaxy-dev] galaxy local installation

galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of fernandez Edgar Sent: Thursday, 12 December 2013 4:31 AM To: galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu> Subject: [galaxy-dev] galaxy local in

Re: [galaxy-dev] galaxy local installation

Hi Edgar please find my comments within your text below: On 12/11/2013 06:30 PM, fernandez Edgar wrote: Hello, My name is Edgar Fernandez. I’m a sys. admin. at University of Montreal. I’ve been ask by a teacher to check out Galaxy. So I’ve installed locally on my computer galaxy (I’m running

Re: [galaxy-dev] galaxy local installation

013 4:31 AM To: galaxy-...@bx.psu.edu Subject: [galaxy-dev] galaxy local installation Hello, My name is Edgar Fernandez. I'm a sys. admin. at University of Montreal. I've been ask by a teacher to check out Galaxy. So I've installed locally on my computer galaxy (I'm running

Re: [galaxy-dev] Galaxy wrappers for CLC Assembly Cell (CLCbio)

On Mon, Nov 18, 2013 at 4:29 PM, Peter Cock wrote: > On Mon, Nov 18, 2013 at 4:23 PM, Eric Kuyt wrote: >> Hi Peter, it turns out we only have a workbench licence, the clc_assembler >> packaged with the workbench is called ./clc_assembler_ilo >> >> which has the man page below, do you think this i

Re: [galaxy-dev] Galaxy Library: problem with directories which are symlinks

_import_dir" directory)? > > > Thanks in advance to all, > > Mish > > > > > > > >> Date: Thu, 28 Nov 2013 15:06:47 -0600 >> Subject: Re: [galaxy-dev] Galaxy code: data libraries >> From: chil...@msi.umn.edu >> To: mish...@hotmai

[galaxy-dev] Galaxy Library: problem with directories which are symlinks

wn). Is there a way to force Galaxy to "see" directories which are symlinks ( in the "user_library_import_dir" directory)? Thanks in advance to all, Mish > Date: Thu, 28 Nov 2013 15:06:47 -0600 > Subject: Re: [galaxy-dev] Galaxy code: data libraries > From: c

Re: [galaxy-dev] Galaxy code: data libraries

Hi John, It works very fine. Thank you again for your help, very useful :). Have a nice day, Mish From: mish...@hotmail.com To: chil...@msi.umn.edu Date: Mon, 2 Dec 2013 08:51:28 + CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy code: data libraries Hi John, Thank

Re: [galaxy-dev] [Galaxy-ZBIT] Help needed in Galaxy Uploading files.

Dear Dr Johannes,Alot of thanks for you but i already sent the same issue to galaxy-dev@lists.bx.psu.edu the galaxy mailing list without reply i am so sorry for disturbance Best Regards, https://www.mcpvirtualbusinesscard.com/VBCServer/elsayedhegazy/interactivecardEl-Sayed HegazyIT Manager at

Re: [galaxy-dev] Galaxy code: data libraries

Hi John, Thank you very much for your reply! I will try this, and inform you if it works correctly. Thank you again, Mish > Date: Thu, 28 Nov 2013 15:06:47 -0600 > Subject: Re: [galaxy-dev] Galaxy code: data libraries > From: chil...@msi.umn.edu > To: mish...@hotmail.com >

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