|
8
|
1 <?xml version="1.0"?>
|
|
0
|
2 <tool_dependency>
|
|
8
|
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" />
|
|
|
5 </package>
|
|
0
|
6 <package name="blat" version="35x1">
|
|
|
7 <install version="1.0">
|
|
|
8 <actions>
|
|
2
|
9 <!-- finally go back to the original version and compile blat and the entire server from source
|
|
|
10 Thanks to Nicola Soranzo.
|
|
|
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.
|
|
|
13 -->
|
|
9
|
14 <action type="shell_command">git clone git://genome-source.cse.ucsc.edu/kent.git</action>
|
|
|
15 <action type="shell_command">git reset --hard 84614918e462d7750a8f56e5ce9540c623b87b48</action>
|
|
|
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">
|
|
|
18 <package name="libpng" version="1.6.7" />
|
|
|
19 </repository>
|
|
|
20 </action>
|
|
|
21 <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 $INSTALL_DIR/.ccache/</action>
|
|
2
|
22 <action type="set_environment">
|
|
8
|
23 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
|
|
|
24 <environment_variable action="set_to" name="BLAT_PATH">$INSTALL_DIR</environment_variable>
|
|
0
|
25 </action>
|
|
|
26
|
|
1
|
27
|
|
0
|
28 </actions>
|
|
|
29 </install>
|
|
|
30 <readme>
|
|
1
|
31 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
|
|
0
|
33
|
|
1
|
34 Please note that the BLAT source and executables are freely available for
|
|
|
35 academic, nonprofit and personal use. Commercial licensing information is
|
|
|
36 available on the Kent Informatics website (http://www.kentinformatics.com/).
|
|
0
|
37 </readme>
|
|
|
38 </package>
|
|
|
39 </tool_dependency>
|
