tool_dependency_dir not being picked up?
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"> <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:$PATH export PATH Galaxy log messages when invoking my test tool: galaxy.tools DEBUG 2012-05-31 21:59:17,349 Dependency galaxy_test galaxy.tools WARNING 2012-05-31 21:59:17,349 Failed to resolve dependency on 'galaxy_test', ignoring If I manually source the env.sh file , my test.sh is found and executes as appropriately. Where am I going wrong? Thanks much! Ann
On May 31, 2012, at 11:19 PM, Ann Black-Ziegelbein wrote:
Hi -
I have been trying to run a quick test using the tool_dependency_dir configuration option to prove out how it works ... but unfortunately I can't get it to function right. I was hoping someone could point out my error. I have written a simple tool in galaxy, version_test, that will just echo out a version number to a text file so I can test out tool dependencies and install locations. But my required package is not getting resolved by galaxy....
Snippet from my configuration file: # Directory which contains dependent tool binaries or a env.sh to set env vars in order to find specific versions. tool_dependency_dir = /opt
My simple tool:
<tool id="version_test" name="version_test" version="1.0.0"> <requirements> <requirement type="package">galaxy_test</requirement> </requirements> <description>provides simple stats on BAM files</description> <command>test.sh "$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?
Hi Ann, 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' attribute. e.g.: % ln -s 1.0 default % mv env.sh 1.0 --nate
Thanks much!
Ann ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
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Ann Black-Ziegelbein -
Nate Coraor