| Previous changeset 2:4d701c67592a (2013-07-08) Next changeset 4:9195f99fecdd (2013-07-08) |
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Commit message:
Deleted selected files |
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removed:
tool_dependencies.xml |
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| diff -r 4d701c67592a -r 203bda4cf122 tool_dependencies.xml --- a/tool_dependencies.xml Mon Jul 08 22:03:50 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,55 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="R" version="2.15.1"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz</action> - <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> - <action type="shell_command">make</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme>You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R.</readme> - </package>s - <package name="samtools" version="0.1.18"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action> - <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>misc/maq2sam-long</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme>Compiling SAMtools requires the ncurses and zlib development libraries.</readme> - </package> - <package name="rseqc" version="2.3.7"> - <install version = "1.0"> - <action type="download_by_url">http://sourceforge.net/projects/rseqc/files/RSeQC-2.3.7.tar.gz</action> - <action type="shell_command">python setup.py install</action> - <action action="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/lib/rseqc - </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#. - </readme> - </package> - -</tool_dependency> |