Mercurial > repos > devteam > package_freebayes_0_9_6_9608597d

comparison tool_dependencies.xml @ 0:7615ee9e216d draft default tip

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Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
author devteam
date Mon, 16 Dec 2013 16:30:37 -0500
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-1:000000000000 0:7615ee9e216d
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">
4 <install version="1.0">
5 <actions_group>
6 <actions architecture="i386" os="linux">
7 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/freebayes/freebayes-0.9.6_9608597d-Linux-i686.tgz</action>
8 <action type="move_directory_files">
9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
11 </action>
12 </actions>
13 <actions architecture="x86_64" os="linux">
14 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/freebayes/freebayes-0.9.6_9608597d-Linux-x86_64.tgz</action>
15 <action type="move_directory_files">
16 <source_directory>.</source_directory>
17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
18 </action>
19 </actions>
20 <actions architecture="x86_64" os="darwin">
21 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/freebayes/freebayes-0.9.6_9608597d-Darwin-x86_64.tgz</action>
22 <action type="move_directory_files">
23 <source_directory>.</source_directory>
24 <destination_directory>$INSTALL_DIR/bin</destination_directory>
25 </action>
26 </actions>
27 <actions>
28 <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
29 <action type="shell_command">git checkout 9608597d12e127c847ae03aa03440ab63992fedf</action>
30 <action type="shell_command">git submodule update --recursive</action>
31 <action type="shell_command">make || ( make clean &amp;&amp; sed -i.bak -e &apos;s:LIBS = -lz -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix:LIBS = -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz:g&apos; src/Makefile &amp;&amp; make )</action>
32 <action type="move_directory_files">
33 <source_directory>bin</source_directory>
34 <destination_directory>$INSTALL_DIR/bin</destination_directory>
35 </action>
36 </actions>
37 <action type="set_environment">
38 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
39 </action>
40 </actions_group>
41 </install>
42 <readme>
43 FreeBayes requires g++ and the standard C and C++ development libraries.
44 Additionally, cmake is required for building the BamTools API.
45 </readme>
46 </package>
47 </tool_dependency>