Mercurial > repos > nilesh > somatic_sniper
changeset 13:931e995eafc3 draft
Deleted selected files
author | nilesh |
---|---|
date | Fri, 28 Jun 2013 17:45:24 -0400 (2013-06-28) |
parents | 4c19920a7497 |
children | 2deab63204bf |
files | tool_dependencies.xml |
diffstat | 1 files changed, 0 insertions(+), 40 deletions(-) [+] |
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--- a/tool_dependencies.xml Fri Jun 28 17:17:48 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +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>$INSTALL_DIR/bin/samtools</destination_directory> - </action> - - <!-- Somatic Sniper --> - <action type="download_file">https://github.com/genome/somatic-sniper/archive/master.zip</action> - <action type="download_file">https://github.com/genome/build-common/tarball/master</action> - <action type="shell_command">unzip master.zip</action> - <action type="shell_command">tar -xzvf master</action> - <action type="shell_command">rm -rf somatic-sniper-master/build-common/</action> - <action type="shell_command">mv genome-build-common-077bd57/ somatic-sniper-master/build-common/</action> - <action type="shell_command">cmake -D Samtools_INCLUDE_DIR:PATH=$INSTALL_DIR/bin/samtools somatic-sniper-master/ && make</action> - <action type="move_directory_files"> - <source_directory>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>