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.gu...@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. ;-) > > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > > ___________________________________________________________ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
