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comparison tool_dependencies.xml @ 29:907d4b021ff6

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author nilesh
date Thu, 11 Jul 2013 12:31:33 -0400
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children b5d2f575ccb6
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28:6e438a559a10 29:907d4b021ff6
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="R" version="2.15.1">
4 <install version="1.0">
5 <actions>
6 <action type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz</action>
7 <action type="shell_command">./configure --prefix=$INSTALL_DIR/lib</action>
8 <action type="shell_command">make</action>
9 <action type="move_file">
10 <source>bin/R</source>
11 <destination>$INSTALL_DIR/lib/bin</destination>
12 </action>
13 <action type="set_environment">
14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
15 </action>
16 </actions>
17 </install>
18 <readme>
19 You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R.
20 </readme>
21 </package>
22 <package name="samtools" version="0.1.18">
23 <install version="1.0">
24 <actions>
25 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
26 <action type="shell_command">make</action>
27 <action type="move_file">
28 <source>samtools</source>
29 <destination>$INSTALL_DIR/bin</destination>
30 </action>
31 <action type="move_file">
32 <source>bcftools/bcftools</source>
33 <destination>$INSTALL_DIR/bin</destination>
34 </action>
35 <action type="set_environment">
36 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
37 </action>
38 </actions>
39 </install>
40 <readme>Both BCFTools and Samtools installed in this dependency.Compiling SAMtools requires the ncurses and zlib development libraries.</readme>
41 </package>
42 <package name="rseqc" version="2.3.7">
43 <install version = "1.0">
44 <actions>
45 <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action>
46 <action type="shell_command">python setup.py install --root $INSTALL_DIR/lib/rseqc</action>
47 <action type="set_environment">
48 <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/rseqc/usr/local/lib/python2.7/site-packages
49 </action>
50 <action type="set_environment">
51 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/lib/rseqc/usr/local/bin</environment_variable>
52 </action>
53 </actions>
54 </install>
55 <readme>
56 RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html#.
57 </readme>
58 </package>
59
60 </tool_dependency>