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" <g...@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 >>> >>> <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: >>> >>> http://lists.bx.psu.edu/ >> >> >> ___________________________________________________________ >> 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: >> >> http://lists.bx.psu.edu/ > > > This email (including any attachments or links) may contain > confidential and/or legally privileged information and is > intended only to be read or used by the addressee. If you > are not the intended addressee, any use, distribution, > disclosure or copying of this email is strictly > prohibited. > Confidentiality and legal privilege attached to this email > (including any attachments) are not waived or lost by > reason of its mistaken delivery to you. > If you have received this email in error, please delete it > and notify us immediately by telephone or email. Peter > MacCallum Cancer Centre provides no guarantee that this > transmission is free of virus or that it has not been > intercepted or altered and will not be liable for any delay > in its receipt. > > ___________________________________________________________ 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: http://lists.bx.psu.edu/
