- galaxy-dev - lists.galaxyproject.org

homebrew python
by Joshua Udall 29 Mar '14

29 Mar '14

For various reasons, I installed a Homebrew of python instead of the system version on OSX 10.9.2. Now, when galaxy initializes, it isn't looking in the right location for eggs (or they aren't placed in the right spot on my system). I was able to manually install several of the eggs and the galaxy startup would move to the next egg until here. Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of WebHelpers) cannot be fetched Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 37, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/galaxy/galaxy-old3/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "build/bdist.macosx-10.9-x86_64/egg/pkg_resources.py", line 588, in resolve The `plugin_env` should be an ``Environment`` instance that contains pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. I know numpy, WebHelpers, MarkupSafe are installed and they are current (maybe too current?) ... what would be a good way to resolve the conflict? The manual download below fails on a dozen packages or so. sudo python ./scripts/make_egg_packager.py py2.7-macosx-10.9-x86_64-ucs2 Using Python interpreter at /usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python, Version 2.7.6 (default, Mar 24 2014, 14:39:40) [GCC 4.2.1 Compatible Apple LLVM 5.1 (clang-503.0.38)] This platform is 'py2.7-macosx-10.9-x86_64-ucs2' Override with: make_egg_packager.py <forced-platform> Completed packager is 'egg_packager-py2.7-macosx-10.9-x86_64-ucs2.py'. To fetch eggs, please copy this file to a system with internet access and run with: python egg_packager-py2.7-macosx-10.9-x86_64-ucs2.py -- Joshua Udall Assistant Professor 295 WIDB Plant and Wildlife Science Dept. Brigham Young University Provo, UT 84602 801-422-9307 Fax: 801-422-0008 USA

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ERROR executing tool
by virginia dalla via 29 Mar '14

29 Mar '14

Hi, I tried to GROOMER my fastq data in fastq data, and galaxy did not allowed me:Error executing tool: objectstore, __call_method failed: get_filename on , kwargs: {}could you please help me?Thank you viR

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Forward of moderated message
by galaxy-user-bounces＠lists.bx.psu.edu 29 Mar '14

29 Mar '14

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restarting Galaxy without affecting jobs
by David Hoover 29 Mar '14

29 Mar '14

What are the configuration steps required for allowing a local Galaxy installation to be restarted without affecting currently running jobs? I have Galaxy using DRMAA to submit jobs onto a backend cluster. I thought that enable_job_recovery = True should allow this, but in a few tests I have found that although the batch jobs completed, Galaxy lost track of the jobs and classified them as failed. Would track_jobs_in_database = True be required? This is currently set to the default 'None'. Our local Galaxy installation has become quite busy, and restarts are not possible without forcing users to restart their jobs. David Hoover Helix Systems Staff

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HELP: universe_wsgi.ini and job_conf.xml for installation using local and PBS pro cluster.
by Luca Toldo 29 Mar '14

29 Mar '14

Dear Galaxians, I'd greatly appreciate if someone that has a running instance of galaxy using local computing power and as well remote nodes (accessed with PBS Pro) could share the files universe_wsgi.ini job_conf.xml I've been trying very hard but failed to make noticeable progress. I have a locally properly running galaxy server, have a properly running (commandline) qsub to a PBS Pro cluster, I have few tools that I would like to run on the cluster, while the majority of tools should run on the local instance (and they do so well already). Thankyou for your patience and knowledge sharing effort.

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Globus World 2014
by Ravi K Madduri 29 Mar '14

29 Mar '14

Dear All I wanted to send a note to folks about Globus World 2014. I apologize before hand for spamming both the developer list and the users list also but I thought this may be relevant to folks on the lists. Please let me know if you have any questions. GlobusWorld is this year’s biggest gathering of all things Globus. GlobusWorld 2014 features a Using Globus Genomics to Accelerate Analysis Tutorial, and a full half day on Globus Genomicsin the main meeting, including a keynote by Nancy Cox and these accepted talks: Globus Genomics: Enabling high-throughput cloud-based analysis and management of NGS data for Translational Genomics research at Georgetown, by Yuriy Gusev, Improving next-generation sequencing variants identification in cancer genes using Globus Genomics, by Toshio Yoshimatsu Globus Genomics: A Medical Center's Bioinformatics Core Perspective, by Anoop Mayampurath Building a Low-budget Public Resource for Large-scale Proteomic Analyses, by Rama Raghavan Globus Genomics is a Globus and Galaxy based platform for genomic analysis. GlobusWorld is being held April 15-17, in Chicago. And, GCC2014 is a Silver Sponsor of GlobusWorld. -- Ravi K Madduri MCS, Argonne National Laboratory Computation Institute, University of Chicago

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tophat2 install
by Briand, Sheldon 28 Mar '14

28 Mar '14

Hi, I ran into a problem installing tophat2 here: tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found I have only used the interface to do the installation (no manual deletes). The rest of the dependencies for tophat2 installed just fine. Repairing the repository doesn't make any difference. Thanks! -Sheldon Sheldon Briand NRC Research Computing Support Analyst Research Computing Support / Soutien Informartique a la Recherche Operations, Science Portfolio / Operations, Portefeuil des sciences SSC-NRC / SPC-CNRC Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford Halifax, NS B3H 3Z1 902 426-1677 sheldon.briand(a)ssc-spc.gc.ca

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minimus2 wrapper
by Peter Cock 28 Mar '14

28 Mar '14

Hi Edward, Are you still working on your minimus2 wrapper? It does the basics very nicely taking FASTA files as input (hiding the conversion into AMOS format internally): http://toolshed.g2.bx.psu.edu/view/edward-kirton/minimus2 One minor improvement is the prefix parameters should be conditional rather than always shown (just some XML tweaking). I could do that, but where do you keep the upstream repository for your wrappers? I'm presuming these are your accounts on GitHub and BitBucket: https://bitbucket.org/eskirton & https://github.com/eskirton Also I would like to see options for setting the parameters (REFCOUNT, OVERLAP, CONSERR, MINID, MAXTRIM) for when the default values do not work. That means XML additions and some Perl wrapper work (outside my comfort zone). Thanks, Peter

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How to write test cases for custom tool
by Janaki Rama Rao Gollapudi 28 Mar '14

28 Mar '14

Hi, I have implemented a custom tool which will parse a given string in to expected format. Installed this custom tool into galaxy and was able to run successfully. I would like to add test cases to this tool, can you please provide me resources to write test cases for this custom tool. Is this tool need functional, unit, integration test cases ? I am not sure about which test cases needed for this tool. Thanks, JanakiRam

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Citing Galaxy + Toolshed in an app note of a small tool
by Assaf Gordon 28 Mar '14

28 Mar '14

Hello Galaxy People! (it's been a while since I've last been here... a pleasure to be back). I intend to publish a small command-line utility, which will also be available through Galaxy Toolshed. It'll be a small application note, so not a lot of space for many citations. The relevant sentence would read something like: "The tool is also available for the Galaxy Bioinformatics Platform [Cite1], with automatic installation provided though the Galaxy Tool Shed [Cite2]". What should I use for [cite1 (galaxy) and [cite2 (toolshed)], out of this impressive long list of publications: https://wiki.galaxyproject.org/CitingGalaxy Thanks! -gordon

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