Mercurial > repos > nilesh > rseqc
diff tool_dependencies.xml @ 32:580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
| author | lparsons |
|---|---|
| date | Mon, 07 Oct 2013 15:01:13 -0400 |
| parents | cc5eaa9376d8 |
| children | 073c77ce5e94 |
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--- a/tool_dependencies.xml Wed Oct 02 02:20:04 2013 -0400 +++ b/tool_dependencies.xml Mon Oct 07 15:01:13 2013 -0400 @@ -1,49 +1,25 @@ <?xml version="1.0"?> <tool_dependency> - <package name="R" version="2.11.0"> + <package name="R" version="3.0.1"> + <repository changeset_revision="7473992d1f38" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="numpy" version="1.7.1"> + <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="rseqc" version="2.3.7"> <install version="1.0"> <actions> - <action type="download_by_url">http://cran.rstudio.com/src/base/R-2/R-2.11.0.tar.gz</action> - <action type="shell_command"> - ./configure --enable-R-shlib \ - --with-readline=no \ - --with-x=no \ - --prefix=$INSTALL_DIR \ - --libdir=$INSTALL_DIR/lib \ - --disable-R-framework - </action> - <action type="shell_command">make && make install</action> + <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action> + <action type="shell_command">python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action> <action type="set_environment"> - <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable> - <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lib/R/bin</environment_variable> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> - R is a free software environment for statistical computing and graphics. - NOTE: See custom compilation options above - </readme> - </package> - <package name="numpy" version="1.7.1"> - <repository toolshed="http://toolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="iuc" changeset_revision="74c21f9bdc39" /> - </package> - <package name="rseqc" version="2.3.7"> - <install version = "1.0"> - <actions> - <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action> - <action type="shell_command">python setup.py install --root $INSTALL_DIR --prefix . --install-lib lib</action> - <action type="set_environment"> - <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html#. - Requires gcc, python, numpy, and R + RSeQC version 2.3.7, documentation available at http://dldcc-web.brc.bcm.edu/lilab/liguow/CGI/rseqc/_build/html/index.html. + Requires gcc and python. </readme> </package>