Hello Bjorn,
From your comments, it seems you are looking for a way to define a tool dependency that is included in the contents of the repository when it is installed from the tool shed. If this is the case, then your tool_dependencies.xml tag set needs to be changed to the following.
<tool_dependency> <set_environment version="1.0"> <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> </tool_deppendency> All of the details for how to define your tool configs and dependencies included in your repository like this are available in the following tool shed wiki page. http://wiki.g2.bx.psu.edu/ToolShedToolFeatures#Finding_dependencies_included... Thanks very much for contributing - I'll take a look at this patch and integrate part or all of it into the next release if appropriate. Greg Von Kuster On Oct 15, 2012, at 1:15 PM, Björn Grüning wrote:
Hi,
i'm writing a galaxy wrapper for bismark and trim-galore. Both are plain perl scripts, that wraps around other dependencies (e.g. Bowtie). The idea was to include the perl-scripts directly in the galaxy-wrapper and update the PATH to the REPOSITORY_INSTALL_DIR in the tool_dependency.xml file.
---- <package name="bismark" version="0.7.7"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable> </action> </actions> </install> <readme> bismark, bismark_genome_preparation and bismark_methylation_extractor are shipped with that wrapper </readme> </package> ----
Unfortunately, that was not supported because the toolshed expected at least one "action_type". The attached patch should add that feature.
Furthermore, bowtie2 is only available as zip archive and afaik that was not handled in the toolshed. The attached patch also added check_zipfile(), extract_zip() and zip_extraction_directory() to fully support zip archives.
Thanks! Bjoern
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