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_shed>salk.bccdc.med.ubc.ca/toolshed</tool_shed>
<repository_name>ffp_phylogeny</repository_name>
<repository_owner>ddooley</repository_owner>
<installed_changeset_revision>eb1924fbd3ba</installed_changeset_revision>
<id>salk.bccdc.med.ubc.ca/toolshed/repos/ddooley/ffp_phylogeny/ffp_phylogeny/0.1.00</id>
<version>0.1.00</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_shed>salk.bccdc.med.ubc.ca/toolshed</tool_shed>
<repository_name>versioned_data</repository_name>
<repository_owner>damion</repository_owner>
<installed_changeset_revision>e9ebe2959300</installed_changeset_revision>
<id>salk.bccdc.med.ubc.ca/toolshed/repos/damion/versioned_data/versioned_data/0.1.00</id>
<version>0.1.00</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
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