April 2014 - galaxy-dev - lists.galaxyproject.org

bug_losing_links_box
by Mélanie Hachet 19 Apr '14

19 Apr '14

Hello, I would like to report a bug. I'm using galaxy in local and I was detected this bug 2 months ago. First, several inputs are necessary for a box (tool) in order to create a workflow. Then, the workflow is saved with several links for one box. So I launched the workflow but i can put only one input. When I looked the workflow, only one link is kept (the last one marked), others aren't kept. However the script corresponding to the box run well independently. If you need any further information, feel free to contact me. Best regards. Mélanie Hachet

2 1

Error Downloading Reference Genomes using Manage Local Data ( AttributeError: 'JobManager' object has no attribute 'deferred_job_queue')
by John Lockhart 18 Apr '14

18 Apr '14

I am attempting to set up a local instance of Galaxy for a bioinformatics lab, but have been unable to add reference genomes to the instance due to this error. I've tried redoing the install, but still receive the error. Any solutions or alternative methods of installing genomes to local instances would be very appreciated. Traceback: URL: http://localhost:8080/data_admin/download_build File '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 377 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/data_admin.py', line 134 in download_build jobid = trans.app.job_manager.deferred_job_queue.plugins['GenomeTransferPlugin'].create_job( trans, url, dbkey, longname, indexers ) AttributeError: 'JobManager' object has no attribute 'deferred_job_queue'

1 0

Functional Tests and ftype
by Saket Choudhary 18 Apr '14

18 Apr '14

I happened to copy Peter's .travis.yml for running tests for some of my packages. However the process has not been smooth at all. See : https://travis-ci.org/saketkc/galaxy_tools/jobs/23166678#L908 AssertionError: Attempting to set field 'input' to value '['condel_input.tabular']' in form 'tool_form' threw exception: cannot find value/label "condel_input.tabular" in list control I am already passing it the correct ftype : https://github.com/saketkc/galaxy_tools/blob/travis-test/condel_web/condel_… Is there something I am missing? Saket

4 20

User usage stats in local instance
by Alejandro Barrera 18 Apr '14

18 Apr '14

Hi, Apologizes if this is not the right place to ask this sort of questions, but I have been asked to report user usage in our lab’s instance of galaxy. In order to crunch the numbers by user (number of logins per month, number of jobs, memory usage, etc.), I thought that in principle, I could ask that info directly to the database (in our case, a MySQL instance). However, given the complex database schema, it looks like this is not the way to do it (at least, not the easy one...). Does anyone have experience retrieving this information? Many thanks in advance, Alex -- Alejandro Barrera Bioinformatics Developer University of Pennsylvania www.biociphers.org

2 2

Galaxy Hackathon at GCC2014
by Dannon Baker 17 Apr '14

17 Apr '14

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 involved. To that end, we’re thrilled to officially announce the very first Galaxy Hackathon (http://bit.ly/gcc2014hack) The hackathon will be a three day event taking place at Johns Hopkins immediately preceding GCC2014 from June 28th-30th. Do you have a feature you've always wanted to implement? Just want to hack on Galaxy (or Cloudman!) with other folks? The Galaxy Hackathon will be a great opportunity to meet and work closely with other community and Galaxy Team members over the course of three days, culminating in some really great improvements and new features to show off at the Galaxy Community Conference afterward. Participation in the hackathon itself is completely free, but there's limited space so if you're interested and would like to participate please go ahead and book both your lodging and hackathon seat at http://bit.ly/gcc2014hackreg. To help organize ideas and people into more concrete projects, we've also set up a hackathon-specific Trello board that we'd love for everyone to go ahead and start using at https://trello.com/b/3YgU637b/gcc2014-hackathon. The board is public and open to commentary and voting, but to create new cards you’ll need to be added as a member so please note the instructions on the board for that. Finally, we are very happy to have Curoverse (https://curoverse.com) on board as the exclusive Peta level sponsor of the hackathon. If you know of any other group that might be interested in sponsoring at the Giga level please let us know. We hope to see you in June, and can't wait to see what we can accomplish! -Dannon Baker on behalf of the GCC2014 Hackathon Organizing Committee

1 0

User usage stats in local instance
by Alejandro Barrera 17 Apr '14

17 Apr '14

Hi, Apologizes if this is not the right place to ask this sort of questions, but I have been asked to report user usage in our lab’s instance of galaxy. In order to crunch the numbers by user (number of logins per month, number of jobs, memory usage, etc.), I thought that in principle, I could ask that info directly to the database (in our case, a MySQL instance). However, given the complex database schema, it looks like this is not the way to do it (at least, not the easy one...). Does anyone have experience retrieving this information? Many thanks in advance, Alex -- Alejandro Barrera Bioinformatics Developer University of Pennsylvania www.biociphers.org

2 1

Re: [galaxy-dev] galaxy-dev Digest, Vol 94, Issue 22
by Dooley, Damion 17 Apr '14

17 Apr '14

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 testing it via one) because it relies on a galaxy admin managed .loc file to list the generic and customized reporting modules. The (toolshed) reporting tool ships with a .loc file that doesn't reference any customized reports, e.g. blast_reporting_templates.loc.sample is #value name description # Add list of html templates here templates.html_report Standard Report Provides report with sections and table sections And then a galaxy admin adds an entry: # Customized templates listed below templates_custom.html_report Customized report Test customized report Task for getting a customized report in place does require manual steps though: customized module, addition of the .pth file, and editing of the above .loc file. Damion ------------------------------ Message: 4 Date: Wed, 16 Apr 2014 06:47:14 -0500 From: John Chilton <jmchilton(a)gmail.com> To: "Dooley, Damion" <Damion.Dooley(a)bccdc.ca> Cc: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> Subject: Re: [galaxy-dev] Can a tool upload a .loc file that is then ... RENAME: custom galaxy tool python modules Message-ID: <CANwbokfAJCLWH7afNk-s7yZXKcz6pWYVq4Ttn0Q=ueZVFXtHtg(a)mail.gmail.com> Content-Type: text/plain; charset=UTF-8 If this is working it sounds reasonable. I think my approach might be to setup Galaxy inside a virtualenv (as recommended here https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer) and just install your extra dependencies inside that virtualenv using pip. $ . <path_to_virtualenv>/bin/activate $ pip install dependency1 $ pip install dependency2 ... After that you should be able to just do a normal Python import. I think you have another open question about the next steps of this - but just to make it explicit - everything is going to work better in "the Galaxy ecosystem" if you can avoid calling code from tools like this and just use the sort of stock options. For instance - neither of these approaches will work with the tool shed. Sometimes that is not possible - I understand that - but I just thought I would put the disclaimer out there. -John

2 1

problem with bioc_qvalue, Version: 1.34.0
by Tony Kusalik 17 Apr '14

17 Apr '14

Hi, I am having a problem with updating our local Galaxy server, and I am hoping someone can help me. Yesterday I performed a 'hg incoming' command. A bunch of updates were applied, from changeset 12443:ec9d31a8bc04 to changeset 13068:c05752549163. I restarted the server (in daemon mode), but it halted. The content of paster.log instructed me to run sh ./scripts/migrate_tools/0010_tools.sh I did that. That script encountered an error: The following error occurred from the InstallManager while installing tool dependency bioc_qvalue : Error installing tool dependency package bioc_qvalue version 1.34.0: Unable to locate required tool shed repository named package_bioc_qvalue_1_34_0 owned by devteam with revision 11735242a19e. How do I get around this problem? I checked the mailing lists for anyone reporting a problem with "bioc_qvalue" or "11735242a19e" but nothing was turned up. Tony Kusalik

1 0

select both chromosome size and mappable genome size
by Ido Tamir 17 Apr '14

17 Apr '14

Hi, my tool needs both a file with chromosome lengths and the total mappable genome size. I would like to hardcode the mappable genome size per build somewhere. However the user should have to use only one drop down to select both. How can I achieve this? e.g. currently: <param name="FAI" type="select" label="Select chromsome sizes" > <options from_file="chrsize.loc"> <column name="name" index="0"/> <column name="value" index="1"/> </options> </param> with chrsize.loc: mm9 /groups/csf-ngs/wfsys/galaxy/tool-data/shared/ucsc/chrom/mm9.len mm10 /groups/csf-ngs/wfsys/galaxy/tool-data/shared/ucsc/chrom/mm10.len hg19 /groups/csf-ngs/wfsys/galaxy/tool-data/shared/ucsc/chrom/hg19.len dm3 /groups/csf-ngs/wfsys/galaxy/tool-data/shared/ucsc/chrom/dm3.len Currently I multiply the genome size from the fai file by 0.8 to get the mappable size within my tool, but I would like to use more exact numbers per build. thank you very much, ido

1 0

select both chromosome size and mappable genome size
by Service,solexa 17 Apr '14

17 Apr '14

Hi, my tool needs both a file with chromosome lengths and the total mappable genome size. I would like to hardcode the mappable genome size per build somewhere. However the user should have to use only one drop down to select both. How can I achieve this? e.g. currently: <param name="FAI" type="select" label="Select chromsome sizes" > <options from_file="chrsize.loc"> <column name="name" index="0"/> <column name="value" index="1"/> </options> </param> with chrsize.loc: mm9 /groups/csf-ngs/wfsys/galaxy/tool-data/shared/ucsc/chrom/mm9.len mm10 /groups/csf-ngs/wfsys/galaxy/tool-data/shared/ucsc/chrom/mm10.len hg19 /groups/csf-ngs/wfsys/galaxy/tool-data/shared/ucsc/chrom/hg19.len dm3 /groups/csf-ngs/wfsys/galaxy/tool-data/shared/ucsc/chrom/dm3.len Currently I multiply the genome size from the fai file by 0.8 to get the mappable size within my tool, but I would like to use more exact numbers per build. thank you very much, ido

1 0