- galaxy-dev - lists.galaxyproject.org

fix for GATK2 wrapper from IUC
by Geert Vandeweyer 27 Jun '14

27 Jun '14

Hi, There is a missing parameter in the unified genotyer config from the iuc gatk2 wrapper: The following line should be added around line 204 (just before </expand></inputs>): <param name="sample_ploidy" type="integer" value="2" label="Sample Ploidy (number of allles). For tumour, set to 2x the number of expected subclones" help="-ploidy,--sample_ploidy" /> Without this line, activating the advanced analysis options causes the job preparation to fail because there is a reference to it in the <command> section gatk2 wrapper used: version : 8bcc13094767 hg tip: changeset: 3:2553f84b8174 tag: tip user: iuc date: Wed Feb 19 04:39:38 2014 -0500 summary: Uploaded Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer

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setup_venv doesn't honour set_environment_for_install / installing lxml
by Jan Kanis 26 Jun '14

26 Jun '14

In a tool_dependency.xml file I want to install python package lxml in a virtual environment, as a tool I'm building needs it. The python lxml package requires the libxml2 tool dependency. I have added a set_environment_for_install action that refers to the libxml2 repository, but when python/pip tries to install lxml it fails, apparently because it can't find the required headers. This appears to be because the setup_virtualenv action does not include install environment variables. It seems to me that install environment variables should be sourced for every following action that can do nontrivial things, not just shell commands. Alternatively, am I trying to install lxml the wrong way, is there a better way? (I'm running on python 2.6) Jan

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Updated Freebayes Wrapper (0.9.14) - Bug Report
by Lance Parsons 26 Jun '14

26 Jun '14

Thanks for the major update of the Freebayes wrapper, excellent! I've run into two issues, however. 1) When using "set allelic scope" I get the following error: Fatal error: Exit code 1 () freebayes: unrecognized option `--min-repeat-length' did you mean --min-repeat-size ? 2) When using a vcf file as input I get the following error: Fatal error: Exit code 1 () open: No such file or directory [bgzf_check_bgzf] failed to open the file: input_variant_vcf.vcf.gz [tabix++] was bgzip used to compress this file? input_variant_vcf.vcf.gz I'd be happy to help resolve these. Is there a bitbucket repo somewhere to submit pull requests? Also, I'm not sure if this is best sent to this list or put into Trello, etc. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Galaxy mobile site
by MF Rogers 26 Jun '14

26 Jun '14

I hope this isn't a FAQ; I have not yet found the question (or answer) online, though I can't imagine I'm the first to ask: Are there plans to make a mobile version of the Galaxy website? Many of the biologists with whom I work would like to be able to monitor and start Galaxy jobs from their iPhones (or other smart phone). While it is possible to do so using the regular website, a mobile-specific site could make it easier. We searched in vain for an app, but I gather that would be a headache to maintain with such a dynamic website. A mobile site seems the right approach, unless there are good reasons not to try it? We may experiment with creating one for our own local Galaxy installation, but would prefer to use existing code if it's available. Many thanks, -- Dr. Mark Rogers Intelligent Systems Laboratory Department of Engineering Mathematics University of Bristol

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Missing 'shared data' library
by Anna Bruniche-Olsen 26 Jun '14

26 Jun '14

Hi, I’m interested in accessing the 'Tasmanian devil SNPs’ dataset, which I believe should be on your ’shared data’ homepage. It seems to have disappeared. Can you make it accessible, thanks. It is from Miller et al. PNAS (2011) (http://www.pnas.org/content/early/2011/06/23/1102838108) In their paper and on their 'Tasmanian Devil Genome Project’ webpage (http://tasmaniandevil.psu.edu/data_access/index.html) they refer to accessing this SNP dataset using Galaxy. Thanks in advance. Cheers, Anna ------------------------------ Anna Brüniche-Olsen PhD candidate School of Biological Sciences University of Tasmania Private Bag 55 Hobart, Tasmania 7001 Australia Phone: +61 488 330 679 E-mail: annabo(a)utas.edu.au<mailto:annabo@utas.edu.au> www.evogentas.org<http://www.evogentas.org>

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job_working_directory
by Shrum, Donald C 25 Jun '14

25 Jun '14

I'd like to set the job_working_directory to the user's home directory. I'm using an apache proxy with ldap authentication. I'm assuming I need to strip the remote_user_maildomain off the user name to do something like... job_working_directory = ~%user/galaxy_working_directory Is this possible?

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Proposed cd-hit tool dependency change in galaxy
by Qi, Chuyang 25 Jun '14

25 Jun '14

Hi all, When installing and testing the cd-hit tool from jjohnson from the main galaxy toolshed into my local instance of galaxy, I encountered a problem where galaxy cannot find the cd-hit program. The error was: "/bin/sh: 1: cd-hit-est: not found" As I debugged the problem, I found that there is an bug in the tool dependency. It installs the cd-hit programs but never moves the programs into the configurable galaxy install directory. This could cause many problems in the situation where users don't have cd-hit already installed on their computer and must depend on the tool dependency to run the tool. I propose we add the following code to the tool dependency: <action type="move_file"> <source>cd-hit</source> <destination>$INSTALL_DIR</destination> </action> <action type="move_file"> <source>cd-hit-est</source> <destination>$INSTALL_DIR</destination> </action> After I made these changes, I pushed the changes into a new repo on my local toolshed, I managed to successfully install cd-hit into a local and dev-test instance of galaxy and the cd-hit tool ran successfully. Thanks for your understanding, Charles Qi

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Upload files to a data library - Invalid Paths
by Dooley, Damion 25 Jun '14

25 Jun '14

Hi folks, In "Upload files to a data library" form, seems like whatever valid path I enter for linking to data on the server, even with "galaxy" as user and r permissions on the folder and files - I get the "invalid paths" message after submitting? The basic form info: ******************************* Invalid paths: /projects/gia/gia_analysis/blast/homologs_index_Spade_genomes/xml_reports/ Upload option: Upload files from filesystem paths File Format: blastxml Paths to upload /projects/gia/gia_analysis/blast/homologs_index_Spade_genomes/xml_reports/ Preserve directory structure? [yes or no] Copy data into Galaxy? Link to files without copying into Galaxy ******************************* Does anyone know a trick to this? Would be nice to have more helpful error explanation here! My galaxy: 5e605ed6069f+ (stable) release_2014.02.10 . I think it is a pretty normal installation. Thanks for any tips, Regards, Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada

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How does Galaxy differentiate users who have not logged on?
by Melissa Cline 25 Jun '14

25 Jun '14

Hi folks, Quick question. When two different users use the same Galaxy instance without logging in, how does Galaxy keep their identities straight, such that when they come back to their computers the next day, they see only their own workspace and not the other user's workspace? Thanks! Melissa

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Unable to finish job - metadata settings
by Preussner, Jens 25 Jun '14

25 Jun '14

Dear all, I noticed a strange behaviour in our local galaxy installation. First of all, my universe_wsgi.ini contains "retry_metadata_internally = False" and "cleanup_job = always". The tool writes its output simply into the job_working_directory and we move it via && mv static_filename.txt $output in the <command>-tag. This works fine. When restarting the galaxy server and executing the tool after a fresh restart, everything is ok, there are no errors. When executing the same tool a second time, galaxy brings a "tool error" stating that it was unable to finish the job. Nevertheless, the output files are all correct (but marked as red or failed). The error report states: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 997, in finish if ( not self.external_output_metadata.external_metadata_set_successfully( dataset, self.sa_session ) and self.app.config.retry_metadata_internally ): File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py", line 731, in external_metadata_set_successfully rval, rstring = json.load( open( metadata_files.filename_results_code ) ) IOError: [Errno 2] No such file or directory: u'/home/galaxy/galaxy-dist/database/job_working_directory/000/59/metadata_results_HistoryDatasetAssociation_281_oHFjx0' And in the logfile you can find multiple entries like that: galaxy.datatypes.metadata DEBUG 2014-06-25 14:29:35,466 Failed to cleanup external metadata file (filename_results_code) for HistoryDatasetAssociation_281: [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/job_working_directory/000/59/metadata_results_HistoryDatasetAssociation_281_oHFjx0' The if-statement in /home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 997 should evaluate to False, since self.app.config.retry_metadata_internally is set to False in the universe_wsgi.ini but it seems it doesn't in this case? Anyone having experienced such a behavior? Any suggestions how to go on and solve the issue? Many thanks! Jens

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