# HG changeset patch # User nilesh # Date 1372451386 14400 # Node ID ef634ac4ed3e5f86b611710102418e2316d62607 # Parent 3b2b09506aeae53a64bba441c3f94852bb72925f Deleted selected files diff -r 3b2b09506aea -r ef634ac4ed3e tool_dependencies.xml --- a/tool_dependencies.xml Fri Jun 28 16:28:56 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ - - - - - - - http://downloads.sourceforge.net/project/samtools/samtools/0.1.6/samtools-0.1.6.tar.bz2 - sed -i.bak 's/-lcurses/-lncurses/' Makefile - sed -i.bak 's/-lz -L. -lbam/-lbam -lz -L./' Makefile - make - - . - $INSTALL_DIR/bin/samtools - - - http://www.cmake.org/files/v2.8/cmake-2.8.11.1.tar.gz - ./bootstrap - make - make install - - . - $INSTALL_DIR/cmake - - https://github.com/genome/somatic-sniper/archive/master.zip - https://github.com/genome/build-common/tarball/master - unzip master.zip - tar -xzvf master - rm -rf somatic-sniper-master/build-common/ - mv genome-build-common-077bd57/ somatic-sniper-master/build-common/ - cmake -D Samtools_INCLUDE_DIR:PATH=$INSTALL_DIR/bin/samtools somatic-sniper-master/ && make - - bin - $INSTALL_DIR/bin - - - $INSTALL_DIR/bin - - - - - Somatic-sniper compiled version is unstable, for stable version use debian package system apt-get, this install requires cmake and zlib (for samtools) - - - - -