>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.
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
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:
> 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
> <package name="bismark" version="0.7.7">
> <install version="1.0">
> <action type="set_environment">
> <environment_variable name="PATH"
> bismark, bismark_genome_preparation and bismark_methylation_extractor
> are shipped with that wrapper
> 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.
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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: