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comparison tool_dependencies.xml @ 32:580ee0c4bc4e

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Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
author lparsons
date Mon, 07 Oct 2013 15:01:13 -0400
parents cc5eaa9376d8
children 073c77ce5e94
comparison
equal deleted inserted replaced
31:cc5eaa9376d8 32:580ee0c4bc4e
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="R" version="2.11.0"> 3 <package name="R" version="3.0.1">
4 <repository changeset_revision="7473992d1f38" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="numpy" version="1.7.1">
7 <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="rseqc" version="2.3.7">
4 <install version="1.0"> 10 <install version="1.0">
5 <actions> 11 <actions>
6 <action type="download_by_url">http://cran.rstudio.com/src/base/R-2/R-2.11.0.tar.gz</action> 12 <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action>
7 <action type="shell_command"> 13 <action type="shell_command">python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
8 ./configure --enable-R-shlib \
9 --with-readline=no \
10 --with-x=no \
11 --prefix=$INSTALL_DIR \
12 --libdir=$INSTALL_DIR/lib \
13 --disable-R-framework
14 </action>
15 <action type="shell_command">make &amp;&amp; make install</action>
16 <action type="set_environment"> 14 <action type="set_environment">
17 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable> 15 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
18 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> 16 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
19 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable>
20 </action> 17 </action>
21 </actions> 18 </actions>
22 </install> 19 </install>
23 <readme> 20 <readme>
24 R is a free software environment for statistical computing and graphics. 21 RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html.
25 NOTE: See custom compilation options above 22 Requires gcc and python.
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>
38 </action>
39 <action type="set_environment">
40 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
41 </action>
42 </actions>
43 </install>
44 <readme>
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
47 </readme> 23 </readme>
48 </package> 24 </package>
49 25
50 </tool_dependency> 26 </tool_dependency>