Hi -
I have been trying to run a quick test using the tool_dependency_dir
configuration option to prove out how it works ... but unfortunately I
can't get it to function right. I was hoping someone could point out my
error. I have written a simple tool in galaxy, version_test, that will
just echo out a version number to a text file so I could test out tool
dependencies and install locations. But my required package is not
getting resolved by galaxy....
Snippet from my configuration file:
# Directory which contains dependent tool binaries or a env.sh to set
env vars in order to find specific versions.
tool_dependency_dir = /opt
My simple tool:
<tool id="version_test" name="version_test" version="1.0.0">
<requirements>
<requirement type="package">galaxy_test</requirement>
</requirements>
<description>provides simple stats on BAM files</description>
<command>test.sh "$output1"
</command>
<inputs>
<param name="input1" type="data" format="tabular,binary" label="Holder
for input file - not used." />
</inputs>
<outputs>
<data name="output1" format="txt" />
</outputs>
</tool>
My filesystem:
[galaxy@galaxy-0-4:galaxy-dist]$ ls -lat /opt/galaxy_test/
total 20
drwxr-xr-x 3 root root 4096 May 16 14:10 2.0
drwxr-xr-x 3 root root 4096 May 16 14:09 1.0
drwxr-xr-x 4 root root 4096 May 16 14:05 .
-rw-r--r-- 1 root root 50 May 16 14:05 env.sh
drwxr-xr-x 72 root root 4096 May 16 14:04 ..
My env file:
#!/bin/bash
PATH=/opt/galaxy_test/1.0/bin:$PATH
export PATH
Galaxy log messages when invoking my test tool:
galaxy.tools DEBUG 2012-05-31 21:59:17,349 Dependency galaxy_test
galaxy.tools WARNING 2012-05-31 21:59:17,349 Failed to resolve
dependency on 'galaxy_test', ignoring
If I manually source the env.sh file , my test.sh is found and executes
as appropriately.
Where am I going wrong?
Thanks much!
Ann
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