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