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">$REPOSITORY_INSTALL_DIR</environment_variable>
</set_environment>
</tool_deppendency>
All of the details for how to define your tool configs and dependencies
included in your repository like this are available in the following tool shed
wiki page.
http://wiki.g2.bx.psu.edu/ToolShedToolFeatures#Finding_dependencies_included_in_an_installed_repository_at_tool_execution_time
Thanks very much for contributing - I'll take a look at this patch and
integrate part or all of it into the next release if appropriate.
Greg Von Kuster
On Oct 15, 2012, at 1:15 PM, Björn Grüning wrote:
> Hi,
>
> i'm writing a galaxy wrapper for bismark and trim-galore. Both are plain
> perl scripts, that wraps around other dependencies (e.g. Bowtie). The
> idea was to include the perl-scripts directly in the galaxy-wrapper and
> update the PATH to the REPOSITORY_INSTALL_DIR in the tool_dependency.xml
> file.
>
> ----
> <package name="bismark" version="0.7.7">
> <install version="1.0">
> <actions>
> <action type="set_environment">
> <environment_variable name="PATH"
> action="prepend_to">$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
>
> <toolshed_zip.patch>___________________________________________________________
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