Mercurial > repos > jjohnson > kent_283
comparison tool_dependencies.xml @ 0:d13b8a459b19 draft default tip
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| author | jjohnson |
|---|---|
| date | Tue, 14 May 2013 16:42:56 -0400 |
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| -1:000000000000 | 0:d13b8a459b19 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="kent" version="283"> | |
| 4 <install version="1.0"> | |
| 5 <actions> | |
| 6 <action type="download_by_url" target_filename="kent.zip">http://hgdownload.cse.ucsc.edu/admin/jksrc.v283.zip</action> | |
| 7 <action type="shell_command"> | |
| 8 export MACHTYPE=`uname -m`; | |
| 9 export BINDIR=$INSTALL_DIR/bin; mkdir $INSTALL_DIR/bin; | |
| 10 cd src/lib; make; | |
| 11 cd ../jkOwnLib; make; | |
| 12 cd ../blat; make; | |
| 13 cd ../gfClient; make; | |
| 14 cd ../gfServer; make; | |
| 15 cd ../utils; mv makefile makefile.orig; grep -v -E 'pslLiftSubrangeBlat|raSqlQuery|scaffoldFaToAgp' makefile.orig > makefile; make | |
| 16 </action> | |
| 17 <action type="set_environment"> | |
| 18 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 19 </action> | |
| 20 </actions> | |
| 21 </install> | |
| 22 <readme> | |
| 23 This only handles blat for a non-commercial linux system. | |
| 24 | |
| 25 Please note that the Blat source and executables are freely available for | |
| 26 academic, nonprofit and personal use. Commercial licensing information is | |
| 27 available on the Kent Informatics website (http://www.kentinformatics.com/). | |
| 28 </readme> | |
| 29 </package> | |
| 30 | |
| 31 </tool_dependency> |