Mercurial > repos > crs4 > blat
changeset 4:5e43533e3ed9 draft
Use package_blat_35x1 in tool_dependencies.xml. Add readme.rst .
| author | crs4 |
|---|---|
| date | Mon, 25 Nov 2013 04:59:52 -0500 |
| parents | d78b8fe7ca83 |
| children | 34e40c872149 |
| files | readme.rst tool_dependencies.xml |
| diffstat | 2 files changed, 25 insertions(+), 18 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Mon Nov 25 04:59:52 2013 -0500 @@ -0,0 +1,24 @@ +BLAT wrapper +============ + +Install +------- + +This BLAT wrapper let you install `BLAT`_ tool dependency automatically. In order to do this, you need to: + +- have Galaxy release_2013.11.04 or later; +- respect BLAT licensing: BLAT source and executables are freely available for academic, nonprofit and personal use. Commercial licensing information is available on the `Kent Informatics website`_. + +.. _BLAT: http://genome.ucsc.edu/FAQ/FAQblat.html +.. _Kent Informatics website: http://www.kentinformatics.com/ + +Version history +--------------- + +- Release 1 (blat_wrapper 0.2): Initial release in the Tool Shed. +- Release 2 (blat_wrapper 0.2): Add version_command element. Add test case from `Joachim Jacob's blat wrapper`_. Add readme section to tool_dependencies.xml . +- Release 3 (blat_wrapper 0.3): Add the possibility to use locally installed FASTA or 2bit files as database source. +- Release 4 (blat_wrapper 0.3): Depend on `package_blat_35x1`_ instead of compiling BLAT (requires Galaxy release_2013.11.04 or later). + +.. _Joachim Jacob's blat wrapper: http://testtoolshed.g2.bx.psu.edu/view/joachim-jacob/blat +.. _package_blat_35x1: http://toolshed.g2.bx.psu.edu/view/iuc/package_blat_35x1
--- a/tool_dependencies.xml Mon Nov 04 09:06:48 2013 -0500 +++ b/tool_dependencies.xml Mon Nov 25 04:59:52 2013 -0500 @@ -1,23 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="blat" version="35"> -<!-- <repository name="package_blat_35x1" owner="iuc" /> This may be used instead of everything inside <install> when a stable Galaxy release will support the 'download_binary' action type --> - <install version="1.0"> - <actions> - <action type="download_by_url" target_filename="blatSrc.zip">http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip</action> - <action type="shell_command">export MACHTYPE=`uname -m` && export HOME=$INSTALL_DIR && mkdir -p $HOME/bin/$MACHTYPE && make</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin/`uname -m`</environment_variable> - </action> - </actions> - </install> - <readme> -BLAT sequence aligner from the UCSC: http://genome.ucsc.edu/FAQ/FAQblat.html -Git development repository: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git - -Please note that the BLAT source and executables are freely available for -academic, nonprofit and personal use. Commercial licensing information is -available on the Kent Informatics website (http://www.kentinformatics.com/). - </readme> + <repository changeset_revision="84c54f1fa280" name="package_blat_35x1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>