Hi, has anything changed in galaxy in this regard? Any way to modify an environment before a tools is run? I now have a tool relying on R-devel and bioconductor devel, both of which I can load in a module. The tool comes from the toolshed with xml like: <command interpreter="Rscript"> … I don't want to hack around in the tool itself, but simply load the necessary R-version. thank you very much, ido On Sep 13, 2013, at 3:23 AM, "Guest, Simon" <Simon.Guest@agresearch.co.nz> wrote:
Just been reading a bit more about the Galaxy packaging system. Here's a slight modification to what I was suggesting that might fit in a bit better. Apologies for not being more familiar with the existing system before proposing extensions.
Recall that my goal is to support using a system-installed (native) package, at a defined version, which I aim to achieve by loading the appropriate environment module before running a tool.
We still have tool_dependencies.xml defining a package at a particular version, but rather than download and build the source code, there's just a directive that says how to pick up the correct program version at runtime, e.g. which environment module to load.
So instead of the tool_dependencies.xml fragment: <tool_dependency> <package name="bwa" version="0.6.2"> <install version="1.0"> <actions> <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.6.2.tar.bz2</action> <action type="shell_command">make</action> <action type="move_file"> <source>bwa</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> </package> </tool_dependency>
We have something like this (NB: element and attribute names are for illustrative purposes only):
<tool_dependency> <package name="bwa" version="0.6.2"> <use_native> <actions> <action type="module_load">bwa/0.6.2</action> </actions> </use_native> </package> </tool_dependency>
This causes the right thing (module load bwa/0.6.2) to be stuck into the dependencies env.sh file when this package is installed from the toolshed. We could call this toolshed tool native_package_bwa_0_6_2, to avoid confusion with the existing download-and-make one.
We might want a bit of flexibility on what actions are supported (in case we want to support Software Collections, for example).
What do you think?
cheers, Simon
PS: In case it wasn't already clear, solving this problem well is quite important to us here at AgResearch. ;-)
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