November 2011 - galaxy-dev - lists.galaxyproject.org

Installing Galaxy on local server
by Toqa Manasrah 03 Nov '11

03 Nov '11

Hello, I am a graduate student at GSU. I am looking for installing GALAXY on our local server http://alla.cs.gsu.edu/~software. as a result I like my server homepage start with the GALAXY interface, like this one: http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some software tolls that we developed in our department. my primary question is which option I have to choose: Local or cloud? looking forward for your help and directions. Thank you. Tuqa

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galaxy citation_url setting
by Shantanu Pavgi 03 Nov '11

03 Nov '11

Hi, It seems like modification of 'citation_url' in the universe_wsgi.ini config file has no effect in the UI (Help --> How to Cite Galaxy). Is it something hard-coded in the source? -- Thanks, Shantanu.

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Toolshed not showing up
by jjv5 03 Nov '11

03 Nov '11

Hello, I am getting a strange error in attempting to use the main Galaxy toolshed. I am using the latest version: galaxy@monolith:~/galaxy-dist$ hg pull -u -r 338ead4737ba pulling from https://bitbucket.org/galaxy/galaxy-dist/ searching for changes no changes found galaxy@monolith:~/galaxy-dist$ I have uncommented this toolshed line: galaxy@monolith:~/galaxy-dist$ grep shed universe_wsgi.ini tool_config_file = tool_conf.xml,shed_tool_conf.xml The shed_tool file is thus: galaxy@monolith:~/galaxy-dist$ cat shed_tool_conf.xml <?xml version="1.0"?> <toolbox tool_path="../shed_tools"> </toolbox> And galaxy@monolith:~/galaxy-dist$ cat tool_sheds_conf.xml <?xml version="1.0"?> <tool_sheds> <tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/> <tool_shed name="Galaxy test tool shed" url="http://testtoolshed.g2.bx.psu.edu/"/> </tool_sheds> When I log in as Admin, click Admin the Galaxy main tool shed (under Tool Sheds) I get this: Not Found The resource could not be found. No action for /browse_downloadable_repositories I'm not sure where to go from here as I can find no info on this, but it looks like something tiny is messed up. Any help is appreciated. Jim

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GeneTrack-Installation - Version?
by Stefanie Ververs 03 Nov '11

03 Nov '11

Hi everybody, we're hosting our own galaxy instance and the next step should bei the integration of GeneTrack. (Not the tool, that is already included, but the browser, which has to be set up on our own, as i could read on the mailing list.) I've been reading all information on http://genetrack.bx.psu.edu and http://atlas.bx.psu.edu/genetrack/docs/genetrack.html - but I do not really get, which is the current, newest version? The only one to download is available at googlecode (1.0.3) and - according to the information on http://genetrack.bx.psu.edu - there is a newer one (2.0) I tried to run the tests for 1.0.3 but some fail - the logs aren't quite clear about the problem, even on Debug-mode. Could you tell me what version to use and which instructions? Are there limits or other dependencies according to the used python-packages? Hoping for help & thanks in advance, Steffi

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Local Galaxy Instance MarkupSafe error
by Mickael ESCUDERO 03 Nov '11

03 Nov '11

Hi there, I'm getting exactly the same problem with any job running on a TORQUE/PBS cluster. The jobs actually run fine as I can see the output and download it, but it's marked as failed in the galaxy history, with the following message: WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched The command `python -ES ./scripts/fetch_eggs.py` gives nothing as output. If I run the same tools locally there is no problem. Cheers Micka > Message: 5 > Date: Thu, 27 Oct 2011 15:08:17 +1100 > From: Jerico Nico De Leon Revote <jerico.revote(a)monash.edu> > To: galaxy-dev(a)lists.bx.psu.edu > Subject: [galaxy-dev] Local Galaxy Instance MarkupSafe error > Message-ID: > <CAP9ULhYiPxYB2CWtqOSM3MquUu55ARxY5poR1dBaHEj1UcO8UQ(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I'm just doing a simple get->data from UCSC on our local Galaxy > instance and got the following error: > > WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) > cannot be fetched > > The job box then is displayed as red on the history panel. > The job runner states that the job finished normally on the cluster. > Galaxy is checkout from galaxy-central (changeset: 6176:34fffbf01183). > > Thanks, > > Jerico >

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Re Acutal user code
by Chorny, Ilya 02 Nov '11

02 Nov '11

Nate, I have been trying to figure out how to make the changes you suggested (i.e. write output files to the job_working_directory) and then move them over to files but I am having a difficult time navigating the code. If you could point me in the right direction, that would be helpful. I know the lib/galaxy/models/__init__.py initializes the output files but I don't think that is the right place to make the change. This change probably needs to be done in the Job_Wrapper but most of the code is very cryptic to me. Any guidance would be greatly appreciated. These changes should not take very long to implement once I get a handle on the code. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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getting job's index position in the history from database
by Shantanu Pavgi 02 Nov '11

02 Nov '11

I am trying to get job's index in the history panel using SQL query (index number shown in the history when a job is submitted). I am unable to locate the necessary table-column for it. Any pointers in which table-column it is located will be really helpful. -- Thanks, Shantanu.

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Re: [galaxy-dev] [galaxy-user] Queuepool limit problem
by Nate Coraor 02 Nov '11

02 Nov '11

Cinto Queky wrote: > > Hi All, > We encountered queuepool limit problem after running the workflows for a few times. > We have tried to increase these 2 parameters: database_engine_option_pool_size and database_engine_option_max_overflow to 20 and 40 respectively. > Are there other parameters that we can change? Hi Cinto, I've moved this over to galaxy-dev since it concerns a local install. Are you running the workflows concurrently, or sequentially? This shouldn't really happen with only a couple workflows. You could also add: database_engine_option_strategy = threadlocal Thanks, --nate > > Thanks,Cinto > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/

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cufflinks version
by David Hoover 02 Nov '11

02 Nov '11

What version of cufflinks do the current Galaxy wrappers support? The wiki (http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies) says 1.0.1, but our local instance only works with 1.1.0. Can the wiki be updated? David Hoover Helix Systems Staff http://helix.nih.gov

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Re: [galaxy-dev] [galaxy-user] Cannot get rid of custom build error
by Jennifer Jackson 02 Nov '11

02 Nov '11

Hi Jim, I am going to post your question over to the galaxy-dev mailing list (is best for local/cloud instance questions). Would you be able to confirm which version of Galaxy you are running? The latest version of the distribution? http://wiki.g2.bx.psu.edu/News%20Briefs/2011_10_25 "upgrade: % hg pull -u -r 338ead4737ba" Please send your reply as a "reply-all" that includes the galaxy-dev mailing list, but omits the galaxy-user mailing list. Thanks for the additional information, Jen Galaxy team On 11/2/11 4:04 AM, James Vincent wrote: > Hello, > > I've tried to create a custom build (starting from the trackster page) > and clearly made some mistake. I get a NoConverterException error > which is almost certainly my fault putting something wrong in. > However, now the Custom Builds page shows this error and I cannot make > it go away. > > I have a local install, have killed and restarted, logged in and out, > but still this error stays. I cannot try to enter another custom build > because there is nothing on the page except this error. Does anyone > kow how to get rid of this? Any help in getting around this error are > appreciated. > > Jim > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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