[galaxy-dev] Adding options to a tool
Hello all, I am a new Galaxy admin/developer, so if this is as stupid question please be kind. I am trying to add the ability for a user to choose additional parameters for Tophat for Illumina. After analyzing the Python and XML files in /galaxy-dist/tools/ngs_rna, I came to the conclusion that modifying these files would give me the desired results. However, no changes that I make to these files seem to have any effect whatsoever on the user experience inside the Galaxy server. I can not find any other likely candidates inside galaxy-dist. Am I looking in the wrong place? Is it even possible to add parameters to a tool interface? Thanks in advance for any help you can offer. -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Adding options to a tool
Hello Scott, the tool named 'tophat' has been migrated out of distribution to the Tool Shed over a year ago. Which means that if it is in your Galaxy and your Galaxy is newer than a year it must have been installed from the Tool Shed. Tool Shed acts like an app store for Galaxy Tools. The tophat tool is hosted here: https://toolshed.g2.bx.psu.edu/view/devteam/tophat and developed here: https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat However the first thing I would check is whether the newer version of the tool (named tophat2) that we recently updated would suit your needs. You can try it on our Test instance here: https://test.galaxyproject.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.7 Please let me know if you have any questions and thank you for using Galaxy. Martin, Galaxy Team On Wed Feb 11 2015 at 4:36:08 PM Scott Szakonyi scott.b.szakony...@nd.edu wrote: Hello all, I am a new Galaxy admin/developer, so if this is as stupid question please be kind. I am trying to add the ability for a user to choose additional parameters for Tophat for Illumina. After analyzing the Python and XML files in /galaxy-dist/tools/ngs_rna, I came to the conclusion that modifying these files would give me the desired results. However, no changes that I make to these files seem to have any effect whatsoever on the user experience inside the Galaxy server. I can not find any other likely candidates inside galaxy-dist. Am I looking in the wrong place? Is it even possible to add parameters to a tool interface? Thanks in advance for any help you can offer. -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tool test failure - I could use some help...
I was trying to track down why an attempt to test my tool is eventually failing with: ValueError: No such test TestForTool_ffp_phylogeny In my case the tool code is located in a Galaxy's tool shed folder, so I'm guessing that might have something to do with it? Has someone come up with a thorough checklist on issues around this? Tool xml file header: tool id=ffp_phylogeny name=Feature Frequency Profile Phylogeny version=0.1.00 Using John Chilton's ready made sqlite db (though our live server uses a postgres one) export GALAXY_TEST_DB_TEMPLATE=tmp/db_gx_rev_0120.sqlite Command line (recent Update tag latest_2015.01.13 for changeset 0cb6cec4ee57): run_tests.sh -id ffp_phylogeny begins the process alright. *** My galaxy-dist/tool_shed.xml.sample where I understand references to the tool are supposed to go (and I confirmed the tool file absolute path): ?xml version=1.0? toolbox tool_path=../shed_tools section id=bccdc_tools name=BCCDC Tools version= tool file=/usr/local/galaxy/production1/shed_tools/salk.bccdc.med.ubc.ca/toolshed/repos/ddooley/ffp_phylogeny/eb1924fbd3ba/ffp_phylogeny/ffp_phylogeny.xml guid=salk.bccdc.med.ubc.ca/toolshed/repos/ddooley/ffp_phylogeny/ffp_phylogeny/0.1.00 tool_shedsalk.bccdc.med.ubc.ca/toolshed/tool_shed repository_nameffp_phylogeny/repository_name repository_ownerddooley/repository_owner installed_changeset_revisioneb1924fbd3ba/installed_changeset_revision idsalk.bccdc.med.ubc.ca/toolshed/repos/ddooley/ffp_phylogeny/ffp_phylogeny/0.1.00/id version0.1.00/version /tool tool file=salk.bccdc.med.ubc.ca/toolshed/repos/damion/versioned_data/e9ebe2959300/versioned_data/versioned_data.xml guid=salk.bccdc.med.ubc.ca/toolshed/repos/damion/versioned_data/versioned_data/0.1.00 tool_shedsalk.bccdc.med.ubc.ca/toolshed/tool_shed repository_nameversioned_data/repository_name repository_ownerdamion/repository_owner installed_changeset_revisione9ebe2959300/installed_changeset_revision idsalk.bccdc.med.ubc.ca/toolshed/repos/damion/versioned_data/versioned_data/0.1.00/id version0.1.00/version /tool /toolbox Thanks for any pointers! Soon as tests fly, I'll be contributing the tools up to the test tooshed. 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 ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Adding options to a tool
Hi Scott and just double checking, in case you do have an 'old' Galaxy installation: after modifying the xml file (I assume you are talking about tophat_wrapper.xml?): Have you re-loaded the tool? click on 'Reload a tool's configuration' on the administration menu and select the tool Hans-Rudolf Reload a tool's configuration On 02/11/2015 11:00 PM, Martin Čech wrote: Hello Scott, the tool named 'tophat' has been migrated out of distribution to the Tool Shed over a year ago. Which means that if it is in your Galaxy and your Galaxy is newer than a year it must have been installed from the Tool Shed. Tool Shed acts like an app store for Galaxy Tools. The tophat tool is hosted here: https://toolshed.g2.bx.psu.edu/view/devteam/tophat and developed here: https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat However the first thing I would check is whether the newer version of the tool (named tophat2) that we recently updated would suit your needs. You can try it on our Test instance here: https://test.galaxyproject.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.7 Please let me know if you have any questions and thank you for using Galaxy. Martin, Galaxy Team On Wed Feb 11 2015 at 4:36:08 PM Scott Szakonyi scott.b.szakony...@nd.edu mailto:scott.b.szakony...@nd.edu wrote: Hello all, I am a new Galaxy admin/developer, so if this is as stupid question please be kind. I am trying to add the ability for a user to choose additional parameters for Tophat for Illumina. After analyzing the Python and XML files in /galaxy-dist/tools/ngs_rna, I came to the conclusion that modifying these files would give me the desired results. However, no changes that I make to these files seem to have any effect whatsoever on the user experience inside the Galaxy server. I can not find any other likely candidates inside galaxy-dist. Am I looking in the wrong place? Is it even possible to add parameters to a tool interface? Thanks in advance for any help you can offer. -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu http://crc.nd.edu/ _ 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: https://lists.galaxyproject.__org/ https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/__search/mailinglists/ http://galaxyproject.org/search/mailinglists/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/