Mercurial > repos > nilesh > somatic_sniper
changeset 3:4308fb6335c4 draft
Uploaded
author | nilesh |
---|---|
date | Fri, 28 Jun 2013 16:26:19 -0400 (2013-06-28) |
parents | 6c651ff0e91d |
children | 85293d004546 |
files | tool_dependencies.xml |
diffstat | 1 files changed, 46 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jun 28 16:26:19 2013 -0400 @@ -0,0 +1,46 @@ +<?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>$INSTALL_DIR/bin/samtools</destination_directory> + </action> + <!-- CMake --> + <action type="download_by_url">http://www.cmake.org/files/v2.8/cmake-2.8.11.1.tar.gz</action> + <action type="shell_command">./bootstrap</action> + <action type="shell_command">make</action> + <action type="shell_command">make install</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR/cmake + <!-- 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>