Hi all,
Over on the test Tool Shed, I'm trying to include automated installation
of NLStradamus as part of my wrapper for this NLS prediction tool.
This should make things simper for end users, but is also intended to
get the unit tests to pass on the Galaxy Tool Shed setup. The repo is here:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
The unit tests are still failing, just saying:
Fatal error: Exit code 127 ()
/bin/sh: 1: NLStradamus: not found
The tool XML file contains an explicit package dependency:
<requirements>
<requirement type="binary">NLStradamus</requirement>
<requirement type="package" version="1.8">NLStradamus</requirement>
</requirements>
That package dependency is defined using the tool_dependencies.xml
file (in the same repository). My tool_dependencies.xml file should compile
this binary, and have it added to the $PATH. This error message suggests
that this did not work:
<?xml version="1.0"?>
<tool_dependency>
<package name="NLStradamus" version="1.8">
<install version="0.0.1">
<actions>
<action
type="download_by_url">http://www.moseslab.csb.utoronto.ca/NLStradamus/NLStradamus/NLStradamus.1.8.tar.gz</action>
<!-- Although v1.7 used a subfolder in the tar-ball, v1.8 did
not -->
<action type="shell_command">g++ NLStradamus.cpp -o
NLStradamus -O3</action>
<action
type="move_file"><source>NLStradamus</source><destination>$INSTALL_DIR/</destination></action>
<action type="set_environment">
<environment_variable name="PATH"
action="prepend_to">$INSTALL_DIR/bin</environment_variable>
</action>
</actions>
</install>
...
My question is was my tool_dependencies.xml file processed, and if
so did it run without errors, and if so why didn't it work?
If there were errors processing the tool_dependencies.xml then I
would hope the ToolShed would show them (and not silently overlook
this and attempt to run the tests anyway). Is that the case?
Thanks,
Peter
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