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comparison tool_dependencies.xml @ 1:d9ac0d9cb48e

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author nilesh
date Mon, 08 Jul 2013 22:03:22 -0400
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0:e73f30d518f9 1:d9ac0d9cb48e
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=$INSTALL_DIR</action>
8 <action type="shell_command">make</action>
9 <action type="set_environment">
10 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
11 </action>
12 </actions>
13 </install>
14 <readme>You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R.</readme>
15 </package>s
16 <package name="samtools" version="0.1.18">
17 <install version="1.0">
18 <actions>
19 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
20 <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action>
21 <action type="shell_command">make</action>
22 <action type="move_file">
23 <source>samtools</source>
24 <destination>$INSTALL_DIR/bin</destination>
25 </action>
26 <action type="move_file">
27 <source>misc/maq2sam-long</source>
28 <destination>$INSTALL_DIR/bin</destination>
29 </action>
30 <action type="set_environment">
31 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
32 </action>
33 </actions>
34 </install>
35 <readme>Compiling SAMtools requires the ncurses and zlib development libraries.</readme>
36 </package>
37 <package name="rseqc" version="2.3.7">
38 <install version = "1.0">
39 <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action>
40 <action type="shell_command">python setup.py install</action>
41 <action action="move_directory_files">
42 <source_directory>.</source_directory>
43 <destination_directory>$INSTALL_DIR/lib/rseqc
44 </action>
45 <action type="set_environment">
46 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
47 </action>
48 </actions>
49 </install>
50 <readme>
51 RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html#.
52 </readme>
53 </package>
54
55 </tool_dependency>