| Previous changeset 3:203bda4cf122 (2013-07-08) Next changeset 5:c7b32e7f0f4d (2013-07-08) |
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Commit message:
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added:
tool_dependencies.xml |
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| diff -r 203bda4cf122 -r 9195f99fecdd tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jul 08 22:05:14 2013 -0400 |
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| @@ -0,0 +1,55 @@ +<?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> + <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</destination_directory> + </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> |