Mercurial > repos > iuc > package_blat_35x1

comparison tool_dependencies.xml @ 12:c2d5d5117413 draft default tip

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author iuc
date Thu, 12 Feb 2015 11:07:01 -0500
parents 7172d70a3c31
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11:7172d70a3c31 12:c2d5d5117413
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="libpng" version="1.6.7"> 3 <package name="libpng" version="1.6.7">
4 <repository changeset_revision="a0b0e0281cc4" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="blat" version="35x1"> 6 <package name="blat" version="35x1">
7 <install version="1.0"> 7 <install version="1.0">
8 <actions> 8 <actions>
9 <!-- finally go back to the original version and compile blat and the entire server from source 9 <!-- finally go back to the original version and compile blat and the entire server from source
10 Thanks to Nicola Soranzo. 10 Thanks to Nicola Soranzo.
11 The problem is that the binaries are not versioned and we can't guarantee reproducibility. 11 The problem is that the binaries are not versioned and we can't guarantee reproducibility.
12 The source packages are versioned and are stored for a long time. 12 The only way to download the source code of minor releases is from the git repository.
13 --> 13 -->
14 <action type="shell_command">git clone git://genome-source.cse.ucsc.edu/kent.git blat</action> 14 <action type="shell_command">git clone git://genome-source.cse.ucsc.edu/kent.git blat</action>
15 <action type="shell_command">git reset --hard 84614918e462d7750a8f56e5ce9540c623b87b48</action> 15 <action type="shell_command">git reset --hard 84614918e462d7750a8f56e5ce9540c623b87b48</action>
16 <action type="set_environment_for_install"> 16 <action type="set_environment_for_install">
17 <repository changeset_revision="a0b0e0281cc4" name="package_libpng_1_6_7" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu"> 17 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu">
18 <package name="libpng" version="1.6.7" /> 18 <package name="libpng" version="1.6.7" />
19 </repository> 19 </repository>
20 </action> 20 </action>
21 <action type="shell_command">export HOME=$INSTALL_DIR &amp;&amp; export MACHTYPE=`uname -m` &amp;&amp; export PNGINCL=-I${LIBPNG_ROOT}/include &amp;&amp; export PNGLIB="-L${LIBPNG_ROOT}/lib -lpng" &amp;&amp; mkdir -p $HOME/bin/$MACHTYPE &amp;&amp; make -C src/lib/ &amp;&amp; make -C src/jkOwnLib/ &amp;&amp; make -C src/blat/ &amp;&amp; mv $INSTALL_DIR/bin/$MACHTYPE/* $INSTALL_DIR/bin/ &amp;&amp; rm -rf $INSTALL_DIR/.ccache/</action> 21 <action type="shell_command">export HOME=$INSTALL_DIR &amp;&amp; export MACHTYPE=`uname -m` &amp;&amp; export PNGINCL=-I${LIBPNG_ROOT}/include &amp;&amp; export PNGLIB="-L${LIBPNG_ROOT}/lib -lpng" &amp;&amp; mkdir -p $HOME/bin/$MACHTYPE &amp;&amp; make -C src/lib/ &amp;&amp; make -C src/jkOwnLib/ &amp;&amp; make -C src/blat/ &amp;&amp; mv $INSTALL_DIR/bin/$MACHTYPE/* $INSTALL_DIR/bin/ &amp;&amp; rm -rf $INSTALL_DIR/.ccache/</action>
22 <action type="set_environment"> 22 <action type="set_environment">
23 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable> 23 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
24 <environment_variable action="set_to" name="BLAT_PATH">$INSTALL_DIR</environment_variable> 24 <environment_variable action="set_to" name="BLAT_PATH">$INSTALL_DIR</environment_variable>
25 </action> 25 </action>
26
27
28 </actions> 26 </actions>
29 </install> 27 </install>
30 <readme> 28 <readme>
31 BLAT sequence aligner from the UCSC: http://genome.ucsc.edu/FAQ/FAQblat.html 29 BLAT sequence aligner from the UCSC: http://genome.ucsc.edu/FAQ/FAQblat.html
32 Git development repository: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git 30 Git development repository: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git