Hi Peter, Thanks for your thoughts on this. I've created the following Trello card for this enhancement.
https://trello.com/card/galaxy-tool-enhancement-to-accommodate-repository-install-dir/506338ce32ae458f6d15e4b3/636 The priority for the tool shed in the area of tool dependencies like this has been the implementation of features that enable sharing a single dependency across multiple tools in separate repositories, so your scenario is not yet supported. This enhancement would actually be as much (or perhaps more) on the Galaxy end than the tool shed, I think, so there may be more resources available to get to it sooner than I can right now. Of course, someone wil get to it as soon as possible. Thanks again for all of your feedback and insight on this. Greg Von Kuster On Feb 15, 2013, at 12:07 PM, Peter Cock wrote: > On Fri, Feb 15, 2013 at 4:57 PM, Greg Von Kuster <g...@bx.psu.edu> wrote: >> >> >> In this case, your motif.xml file can be configured with the following: >> >> <command interpreter="python"> >> motif.py $fasta_file $tabular_file >> </command> >> <requirements> >> <requirement type="set_environment">MOTIF_DAT_PATH</requirement> >> </requirements> >> >> and your repository will need to include the following tool_dependencies.xml >> file: >> >> <?xml version="1.0"?> >> <tool_dependency> >> <set_environment version="1.0"> >> <environment_variable name="MOTIF_DAT_PATH" >> action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> >> </set_environment> >> </tool_dependency> >> > > That seems overly complicated. Would I not be able to assume that > the motif.xml, motif.py, motif.dat etc are all in the same folder (then > I can just use a relative path to find the data file - nice and easy). > > If not, how about simply defining $REPOSITORY_INSTALL_DIR within > the XML language so I can do this: > > <command interpreter="python">motif.py $fasta_file $tabular_file > $REPOSITORY_INSTALL_DIR/motif.dat</command> > > And/or defining $REPOSITORY_INSTALL_DIR as an environment variable > which I can then use in the script (be it Python, Perl, shell, etc)? > > Thanks, > > Peter > ___________________________________________________________ > 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/ ___________________________________________________________ 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/