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comparison tool_dependencies.xml @ 9:d291dc763c4c

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Add an optional alternative make route for compiling FreeBayes; solves issues seen installing under certain architectures.
author Daniel Blankenberg <dan@bx.psu.edu>
date Wed, 05 Jun 2013 15:00:03 -0400
parents 28e422c589ac
children 07d55d9ea9a4
comparison
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8:28e422c589ac 9:d291dc763c4c
4 <install version="1.0"> 4 <install version="1.0">
5 <actions> 5 <actions>
6 <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> 6 <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
7 <action type="shell_command">git checkout 9608597d12e127c847ae03aa03440ab63992fedf</action> 7 <action type="shell_command">git checkout 9608597d12e127c847ae03aa03440ab63992fedf</action>
8 <action type="shell_command">git submodule update --recursive</action> 8 <action type="shell_command">git submodule update --recursive</action>
9 <action type="shell_command">make</action> 9 <action type="shell_command">make || ( make clean &amp;&amp; sed -i.bak -e &apos;s:LIBS = -lz -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix:LIBS = -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz:g&apos; src/Makefile &amp;&amp; make )</action>
10 <action type="move_directory_files"> 10 <action type="move_directory_files">
11 <source_directory>bin</source_directory> 11 <source_directory>bin</source_directory>
12 <destination_directory>$INSTALL_DIR/bin</destination_directory> 12 <destination_directory>$INSTALL_DIR/bin</destination_directory>
13 </action> 13 </action>
14 <action type="set_environment"> 14 <action type="set_environment">