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comparison tool_dependencies.xml @ 10:07d55d9ea9a4 draft

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Uploaded updated tool dependency definition.
author devteam
date Mon, 16 Dec 2013 16:31:57 -0500
parents d291dc763c4c
children
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9:d291dc763c4c 10:07d55d9ea9a4
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf"> 3 <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">
4 <install version="1.0"> 4 <repository changeset_revision="7615ee9e216d" name="package_freebayes_0_9_6_9608597d" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
5 <actions>
6 <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
7 <action type="shell_command">git checkout 9608597d12e127c847ae03aa03440ab63992fedf</action>
8 <action type="shell_command">git submodule update --recursive</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">
11 <source_directory>bin</source_directory>
12 <destination_directory>$INSTALL_DIR/bin</destination_directory>
13 </action>
14 <action type="set_environment">
15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
16 </action>
17 </actions>
18 </install>
19 <readme>
20 FreeBayes requires g++ and the standard C and C++ development libraries.
21 Additionally, cmake is required for building the BamTools API.
22 </readme>
23 </package> 5 </package>
24 <package name="samtools" version="0.1.18"> 6 <package name="samtools" version="0.1.18">
25 <install version="1.0"> 7 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
26 <actions>
27 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
28 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
29 <action type="shell_command">make</action>
30 <action type="move_file">
31 <source>samtools</source>
32 <destination>$INSTALL_DIR/bin</destination>
33 </action>
34 <action type="move_file">
35 <source>misc/maq2sam-long</source>
36 <destination>$INSTALL_DIR/bin</destination>
37 </action>
38 <action type="set_environment">
39 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
40 </action>
41 </actions>
42 </install>
43 <readme>
44 Compiling SAMtools requires the ncurses and zlib development libraries.
45 </readme>
46 </package> 8 </package>
47 </tool_dependency> 9 </tool_dependency>