I've committed an slightly altered version of your contributed code for
handling tool dependencies that are zip archives in change set
8107:b12140970208, which will be available in the next Galaxy release currently
scheduled for the end of next week. Your code required Python 2.6+, so I made
some changes to support Python 2.5+.
Please let me know if you have additional questions regarding this.
Thanks very much for your contributions!
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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