Mercurial > repos > fcaramia > somatic_sniper
changeset 4:e18402c70a35 draft
Uploaded
author | fcaramia |
---|---|
date | Wed, 19 Jun 2013 02:50:22 -0400 |
parents | d71c18eab8e3 |
children | 9937b182a94c |
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 Wed Jun 19 02:50:22 2013 -0400 @@ -0,0 +1,46 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.6"> + <install version="1.0"> + <actions> + <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_file"> + <source>samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="SAMTOOLS_ROOT" action="set_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + Somatic-sniper only builds with samtools version 0.1.6 + </readme> + </package> + + <package name="somatic-sniper" version="unstable"> + <install version="1.0"> + <actions> + + <action type="shell_command">git clone --recursive git://github.com/genome/somatic-sniper.git</action> + <action type="shell_command">cmake</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>bin/bam-somaticsniper</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> + Somatic-sniper compiled version is unstable, for stable version use debian package system apt-get + </readme> + </package> + + +</tool_dependency>