[Patch] ToolShed support for included tools
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">$REPOSITORY_INSTALL_DIR</environment_variable> </action> </actions> </install> <readme> bismark, bismark_genome_preparation and bismark_methylation_extractor are shipped with that wrapper </readme> </package> ---- Unfortunately, that was not supported because the toolshed expected at least one "action_type". The attached patch should add that feature. Furthermore, bowtie2 is only available as zip archive and afaik that was not handled in the toolshed. The attached patch also added check_zipfile(), extract_zip() and zip_extraction_directory() to fully support zip archives. Thanks! Bjoern
Hello Bjorn,
From your comments, it seems you are looking for a way to define a tool dependency that is included in the contents of the repository when it is installed from the tool shed. If this is the case, then your tool_dependencies.xml tag set needs to be changed to the following.
<tool_dependency> <set_environment version="1.0"> <environment_variable name="PATH" action="prepend_to">$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">$REPOSITORY_INSTALL_DIR</environment_variable> </action> </actions> </install> <readme> bismark, bismark_genome_preparation and bismark_methylation_extractor are shipped with that wrapper </readme> </package> ----
Unfortunately, that was not supported because the toolshed expected at least one "action_type". The attached patch should add that feature.
Furthermore, bowtie2 is only available as zip archive and afaik that was not handled in the toolshed. The attached patch also added check_zipfile(), extract_zip() and zip_extraction_directory() to fully support zip archives.
Thanks! Bjoern
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Hi Bjorn, I've committed an slightly altered version of your contributed code for handling tool dependencies that are zip archives in change set 8107:b12140970208, which will be available in the next Galaxy release currently scheduled for the end of next week. Your code required Python 2.6+, so I made some changes to support Python 2.5+. Please let me know if you have additional questions regarding this. Thanks very much for your contributions! Greg Von Kuster On Oct 15, 2012, at 1:15 PM, Björn Grüning wrote:
Hi,
i'm writing a galaxy wrapper for bismark and trim-galore. Both are plain perl scripts, that wraps around other dependencies (e.g. Bowtie). The idea was to include the perl-scripts directly in the galaxy-wrapper and update the PATH to the REPOSITORY_INSTALL_DIR in the tool_dependency.xml file.
---- <package name="bismark" version="0.7.7"> <install version="1.0"> <actions> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$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
<toolshed_zip.patch>___________________________________________________________ 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:
participants (2)
-
Björn Grüning -
Greg Von Kuster