Hello Franco, These details for defining tool dependency installation for tools contained in tool shed repositories are discussed in the Galaxy tool shed wiki at http://wiki.g2.bx.psu.edu/ToolShedToolFeatures. You can also learn a lot by looking at example tool_dependency.xml files in repositories in the tool shed. These repositories in the main Galaxy tool shed provide some good examples: htseqcount, emboss_5, freebayes, picard Greg Von Kuster On Oct 26, 2012, at 1:49 AM, Franco Caramia wrote:

Hi Greg,

Sorry to ask you something unrelated.

Where can I find documentation about usage and syntax of tags such as : install, package

Is there any available?

There has to be more than just : http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax

Thanks,

Franco

On 26/10/12 1:58 AM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:

...

Hi Bjorn,

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:

...

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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