Mercurial > repos > nilesh > somatic_sniper
changeset 29:f28a3fd3237a draft
Deleted selected files
| author | nilesh |
|---|---|
| date | Mon, 08 Jul 2013 14:47:30 -0400 |
| parents | 1cdfa54068d9 |
| children | 905997f00f92 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 0 insertions(+), 45 deletions(-) [+] |
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--- a/tool_dependencies.xml Mon Jul 08 14:44:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,45 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="somatic-sniper" version="unstable"> - <install version="1.0"> - <actions> - - <!-- Samtools --> - <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.6/samtools-0.1.6.tar.bz2</action> - <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> - <action type="shell_command">sed -i.bak 's/-lz -L. -lbam/-lbam -lz -L./' Makefile</action> - <action type="shell_command">make</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/lib/samtools</destination_directory> - </action> - - <!-- Somatic Sniper --> - <action type="shell_command">git clone --recursive git://github.com/genome/somatic-sniper.git</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/lib</destination_directory> - </action> - <action type="make_directory">$INSTALL_DIR/build</action> - <action type="shell_command">cmake -D Samtools_INCLUDE_DIR:PATH=$INSTALL_DIR/lib/samtools $INSTALL_DIR/lib/somatic-sniper</action> - <action type="shell_command">make</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/build</destination_directory> - </action> - <action type="move_directory_files"> - <source_directory>$install_DIR/build/bin</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> - Somatic-sniper compiled version is unstable, for stable version use debian package system apt-get, this install requires cmake and zlib (for samtools) - </readme> - </package> - - -</tool_dependency>