[galaxy-dev] error installing dependency for tool shed repository.
I've just created a repository in the sandbox and have been trying to test the installation of a dependency my tool needs. The tool needs the python module requests and I've written code. I get an error: STDERR python: can't open file 'setup.py': [Errno 2] No such file or directory I've modeled my code on examples I've found in the tool shed. I've replaced the requests module with other python modules and these are installed ok. I can also download and manually install requests with python setup.py install Any suggestions as to what I may be doing wrong? tool_dependencies.xml: ?xml version=1.0? tool_dependency package name=requests version=1.2.3 install version=1.0 actions action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/requests-1.2.3.tar.gz/action action type=make_directory$INSTALL_DIR/lib/python/action action type=make_directory$INSTALL_DIR/bin/action action type=set_environment environment_variable name=PYTHONPATH action=append_to$INSTALL_DIR/lib/python/environment_variable environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action action type=shell_commandpython setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action /actions /install readme /readme /package /tool_dependency ingTest.xml: tool id=ingTest name=ingTest version=1.0 descriptionTesting Tool Shed/description requirements requirement type=package version=1.2.3requests/requirement /requirements command interpreter=python /command inputs /inputs outputs /outputs help .. class:: infomark /help /tool Thanks, -Curt Curt Palm Data Engineer INGENUITY SYSTEMS | www.ingenuity.com 1700 Seaport Blvd., 3rd Floor | Redwood City, CA 94063 650.381.5084 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] error installing dependency for tool shed repository.
Hi Dave, I made changes giving the suggestions of Ross, I got a different error and that gave me insight as to what was going on. I uploaded new xml: ?xml version=1.0? tool_dependency package name=requests version=1.2.3 install version=1.0 actions action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/re quests-1.2.3.tar.gz/action action type=make_directory$INSTALL_DIR/lib/python/action action type=shell_commandexport PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python amp;amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action action type=set_environment environment_variable name=PYTHONPATH action=append_to$INSTALL_DIR/lib/python/environment_variable environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme /readme /package /tool_dependency And this worked for me. I'm thinking you may have downloaded after I made the changes. -Curt On 8/21/13 6:01 PM, Dave Bouvier d...@bx.psu.edu wrote: Curt, I tried installing the ingtest repository on a local instance of Galaxy, and the requests python module installed without errors. Which revision of Galaxy are you trying to install this repository into, and what kind of environment are you running on that system? --Dave B. Try moving the action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/re quests-1.2.3.tar.gz/action line so it's the one before action type=shell_commandpython setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action I think I've been bitten by this - it seems download_by_url changes the current path but only temporarily so you need to run setup.py immediately as the next step? If this works, please confirm to the entire list - I'm sending this to you just in case I'm full of it :) On Thu, Aug 22, 2013 at 9:12 AM, Curt Palm cp...@ingenuity.com wrote: I've just created a repository in the sandbox and have been trying to test the installation of a dependency my tool needs. The tool needs the python module requests and I've written code. I get an error: STDERR python: can't open file 'setup.py': [Errno 2] No such file or directory I've modeled my code on examples I've found in the tool shed. I've replaced the requests module with other python modules and these are installed ok. I can also download and manually install requests with python setup.py install Any suggestions as to what I may be doing wrong? -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J On 2013-08-21 19:12, Curt Palm wrote: I've just created a repository in the sandbox and have been trying to test the installation of a dependency my tool needs. The tool needs the python module requests and I've written code. I get an error: STDERR python: can't open file 'setup.py': [Errno 2] No such file or directory I've modeled my code on examples I've found in the tool shed. I've replaced the requests module with other python modules and these are installed ok. I can also download and manually install requests with python setup.py install Any suggestions as to what I may be doing wrong? tool_dependencies.xml: ?xml version=1.0? tool_dependency package name=requests version=1.2.3 install version=1.0 actions action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/ requests-1.2.3.tar.gz/action action type=make_directory$INSTALL_DIR/lib/python/action action type=make_directory$INSTALL_DIR/bin/action action type=set_environment environment_variable name=PYTHONPATH action=append_to$INSTALL_DIR/lib/python/environment_variable environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action action type=shell_commandpython setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action /actions /install readme /readme /package /tool_dependency ingTest.xml: tool id=ingTest name=ingTest version=1.0 descriptionTesting Tool Shed/description requirements requirement type=package version=1.2.3requests/requirement /requirements command interpreter=python /command inputs /inputs outputs /outputs help .. class:: infomark /help /tool Thanks, -Curt Curt Palm Data Engineer INGENUITY SYSTEMS | www.ingenuity.com 1700 Seaport Blvd., 3rd Floor | Redwood City
[galaxy-dev] GATK metadata problems
When I try to run a GATK analysis that uses a bam file as input, I get the following error in the html page: Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue. when the input file is a bam file that has not run yet or is still running. So I can not set up multi step analysis or set up a work flow. I searched the mailing lists and could not find info on this, only a thread discussing wanting to use meta data from bam files to set the ref. genomes for GATK tools. is there a solution to this I am using the current version of Galaxy. thanks *** Curtis J. Palm cp...@stanford.edu Stanford Genome Technology Center MC: 8307 office: 650-812-1994cell: 408 858-7849 *** ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Bug in cufflinks_wrapper.xml?
I have been having trouble getting cufflinks to run with the -g or -G parameters via Galaxy. when I select either use reference annotation or use reference annotation as guide from the pulldown menu, cufflinks runs , but the -g or -G is not added to the cufflinks command. I think I have found the problem in the cufflinks_wrapper.xml file. line17#if $reference_annotation.use_ref == use reference annotation: line18-G $reference_annotation.reference_annotation_file line19#end if line20#if $reference_annotation.use_ref == use reference annotation guide: line21-g $reference_annotation_guide.reference_annotation_guide_file . line56 conditional name=reference_annotation line57param name=use_ref type=select label=Use Reference Annotation line58option value=NoNo/option line59option value=Use reference annotationUse reference annotation/option line60option value=Use reference annotation guideUse reference annotation as guide/option line61/param note that Use is capitalized in lines57 and 59 but not in lines 17 and 20. I made these changes in lines 17,20 and 21 and I now get the -G and -g are passed to the cuffflinks command use to Use in lines 17 and 20 reference_annotation_guide.reference_annotation_guide_file to reference_annotation.reference_annotation_guide_file in line 21 line17#if $reference_annotation.use_ref == Use reference annotation: line18-G $reference_annotation.reference_annotation_file line19#end if line20#if $reference_annotation.use_ref == Use reference annotation guide: line21-g $reference_annotation.reference_annotation_guide_file -curt *** Curtis J. Palm cp...@stanford.edu Stanford Genome Technology Center MC: 8307 office: 650-812-1994cell: 408 858-7849 *** ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] problem with build_chrom_db.py
I've been configuring my local instance of galaxy to use trackster according to the instructions on https://bitbucket.org/galaxy/galaxy-central/wiki/Visualization when I run the script: python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/ I get files that begin with: META http-equiv=Content-Script-Type content=text/javascript chr1247249719 chr1_random 166326 ... this causes an error in the browser: Could not load chroms for this dbkey: if i delete the first line META http-equiv=Content-Script-Type content=text/javascript from the .len file, then trackster works fine. I'm thinking there is a new line the input to build_chrom_db.py that is not getting stripped by this script thanks, Curt Palm *** Curtis J. Palm cp...@stanford.edu Stanford Genome Technology Center MC: 8307 office: 650-812-1994cell: 408 858-7849 *** ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
