Related to this thread, my report calc tool needs a few python packages,
but I think they are generic enough to be in python 2.6, 2.7 or 3.x , so
can I specify the packages without specifying the python version? (I'm
looking at the
https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_pyt
hon_2_7_bcbiogff_0_6_2/tool_dependencies.xml file). Or do I need to be
doing something like: <action type="shell_command">pip install
...</action> ? I'm able to upload this to our local toolshed, and it
seems to install ok from there, but I see in test server galaxy log
"galaxy.tools.deps WARNING 2015-12-03 22:23:02,513 Failed to resolve
dependency on 'report_calc', ignoring", though tool still runs (probably
because the python packages were already installed manually previously.)
Much obliged,
Damion
Tool definition file has:
<requirements>
<requirement type="package" version="0.1.0">report_calc</requirement>
</requirements>
tool_dependencies.xml :
<?xml version="1.0"?>
<tool_dependency>
<package name="report_calc" version="0.1.0">
<install version="1.0">
<actions>
<action type="setup_python_environment">
<package>https://pypi.python.org/packages/source/d/dateutils/dateutils
-0.6.6.tar.gz#md5=2ba7fcac03635f1f1cad0d94d785001b</package>
<package>https://pypi.python.org/packages/source/p/pyparsing/pyparsing
-2.0.6.tar.gz#md5=a2d85979e33a6600148c6383d3d8de67</package>
</action>
</actions>
</install>
<readme><![CDATA[
Report Calc
-----------
A python tool to text-mine log and report files for variables and tabular
data, and to create custom reports for this data, as well as triggering
workflow halt based on quality control thresholds. This tool requires the
following additional python packages.
pip install dateutils pyparsing
]]>
</readme>
</package>
</tool_dependency>
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