On May 31, 2012, at 11:19 PM, Ann Black-Ziegelbein wrote:
> 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 can 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">
> <requirement type="package">galaxy_test</requirement>
> <description>provides simple stats on BAM files</description>
> <command>test.sh "$output1"
> <param name="input1" type="data" format="tabular,binary" label="Holder for
> input file - not used." />
> <data name="output1" format="txt" />
> My filesystem:
> [galaxy@galaxy-0-4:galaxy-dist]$ 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:
> 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
> Where am I going wrong?
env.sh should live inside the version directory, and you'll also need a
'default' symlink since your requirement tag doesn't have a 'version'
% ln -s 1.0 default
% mv env.sh 1.0
> Thanks much!
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