Mercurial > repos > nilesh > rseqc

comparison tool_dependencies.xml @ 31:cc5eaa9376d8

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Lance's updates
author nilesh
date Wed, 02 Oct 2013 02:20:04 -0400
parents b5d2f575ccb6
children 580ee0c4bc4e
comparison
equal deleted inserted replaced
30:b5d2f575ccb6 31:cc5eaa9376d8
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="R" version="2.15.1"> 3 <package name="R" version="2.11.0">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions> 5 <actions>
6 <action type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz</action> 6 <action type="download_by_url">http://cran.rstudio.com/src/base/R-2/R-2.11.0.tar.gz</action>
7 <action type="shell_command">./configure --prefix=$INSTALL_DIR/lib</action> 7 <action type="shell_command">
8 <action type="shell_command">make</action> 8 ./configure --enable-R-shlib \
9 <action type="move_file"> 9 --with-readline=no \
10 <source>bin/R</source> 10 --with-x=no \
11 <destination>$INSTALL_DIR/lib/bin</destination> 11 --prefix=$INSTALL_DIR \
12 --libdir=$INSTALL_DIR/lib \
13 --disable-R-framework
14 </action>
15 <action type="shell_command">make &amp;&amp; make install</action>
16 <action type="set_environment">
17 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
18 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
19 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
20 </action>
21 </actions>
22 </install>
23 <readme>
24 R is a free software environment for statistical computing and graphics.
25 NOTE: See custom compilation options above
26 </readme>
27 </package>
28 <package name="numpy" version="1.7.1">
29 <repository toolshed="http://toolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="iuc" changeset_revision="74c21f9bdc39" />
30 </package>
31 <package name="rseqc" version="2.3.7">
32 <install version = "1.0">
33 <actions>
34 <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action>
35 <action type="shell_command">python setup.py install --root $INSTALL_DIR --prefix . --install-lib lib</action>
36 <action type="set_environment">
37 <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
12 </action> 38 </action>
13 <action type="set_environment"> 39 <action type="set_environment">
14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 40 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
15 </action> 41 </action>
16 </actions> 42 </actions>
17 </install> 43 </install>
18 <readme> 44 <readme>
19 You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. 45 RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html#.
46 Requires gcc, python, numpy, and R
20 </readme> 47 </readme>
21 </package> 48 </package>
22 <package name="samtools" version="0.1.18"> 49
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</environment_variable>
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> 50 </tool_dependency>