Hi Galaxians,
I've been scratching a bit my head about how galaxy builds dependency, fruitlessly so far... Here is my problem: I have a local tool (not installed through a toolshed) that makes use of another tool (aragorn) that I installed from the toolshed.
Aragorn requires the aragorn package, as stated in its .xml file:
<requirement type="package" version="1.2.36">aragorn</requirement>
When I run aragorn, it runs fine, and the dependencies are built fine.
galaxy.tools DEBUG 2013-09-05 12:20:14,340 Building dependency shell command for dependency 'aragorn'
Now when I run my tool, which has the exact same requirement line:
<requirement type="package" version="1.2.36">aragorn</requirement>
the dependency is not built correctly, and fail to resolve: galaxy.tools DEBUG 2013-09-05 12:26:22,823 Building dependency shell command for dependency 'aragorn' galaxy.tools WARNING 2013-09-05 12:26:22,823 Failed to resolve dependency on 'aragorn', ignoring
The required package is installed in galaxy-dist/tool-dependency-dir/aragorn/1.2.36/bgruening/trna_prediction/d34f31cbc9dd/ and there is an env.sh there that points correctly to the binaries. Now if I copy that env.sh file into galaxy-dist/tool-dependency-dir/aragorn/1.2.36/, it works fine and the dependency command is built all fine, but it is not done automatically when I install aragorn through the toolshed.
Am I doing something wrong? Missing something somewhere?
Cheers,
Lionel