Mercurial > repos > iuc > package_blat_35x1
diff tool_dependencies.xml @ 9:7dcd799f7b10 draft
Build from git to get version 35x1 instead of 35.
| author | soranzo |
|---|---|
| date | Mon, 10 Feb 2014 12:05:55 -0500 |
| parents | e129755922bd |
| children | 0c6b4862f969 |
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--- a/tool_dependencies.xml Fri Feb 07 05:04:38 2014 -0500 +++ b/tool_dependencies.xml Mon Feb 10 12:05:55 2014 -0500 @@ -11,8 +11,14 @@ The problem is that the binaries are not versioned and we can't guarantee reproducibility. The source packages are versioned and are stored for a long time. --> - <action target_filename="blatSrc.zip" type="download_by_url">http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip</action> - <action type="shell_command">export HOME=$INSTALL_DIR && mkdir -p $HOME/bin/`uname -m` && make MACHTYPE=`uname -m` && mv $INSTALL_DIR/bin/`uname -m`/* $INSTALL_DIR/bin/ && rm $INSTALL_DIR/.ccache/ -rf</action> + <action type="shell_command">git clone git://genome-source.cse.ucsc.edu/kent.git</action> + <action type="shell_command">git reset --hard 84614918e462d7750a8f56e5ce9540c623b87b48</action> + <action type="set_environment_for_install"> + <repository changeset_revision="a0b0e0281cc4" name="package_libpng_1_6_7" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="libpng" version="1.6.7" /> + </repository> + </action> + <action type="shell_command">export HOME=$INSTALL_DIR && export MACHTYPE=`uname -m` && export PNGINCL=-I${LIBPNG_ROOT}/include && mkdir -p $HOME/bin/$MACHTYPE && make -C src/lib/ && make -C src/jkOwnLib/ && make -C src/blat/ && mv $INSTALL_DIR/bin/$MACHTYPE/* $INSTALL_DIR/bin/ && rm -rf $INSTALL_DIR/.ccache/</action> <action type="set_environment"> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable> <environment_variable action="set_to" name="BLAT_PATH">$INSTALL_DIR</environment_variable> @@ -25,19 +31,6 @@ 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 -This reporsitory contains the following binaries: -- blat -- faToNib -- faToTwoBit -- gfClient -- gfServer -- nibFrag -- pslPretty -- pslReps -- pslSort -- twoBitInfo -- twoBitToFa - 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/).