# HG changeset patch # User fcaramia # Date 1371536330 14400 # Node ID c89d9d0234cfb63433d051b6f1ae548c7aa8b56e # Parent e9204226dfc700dc3bdcf12f19d2a6bb56da2be2 Uploaded diff -r e9204226dfc7 -r c89d9d0234cf tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jun 18 02:18:50 2013 -0400 @@ -0,0 +1,82 @@ + + + + + + + http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2 + sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile + make + + samtools + $INSTALL_DIR/bin + + + misc/maq2sam-long + $INSTALL_DIR/bin + + + $INSTALL_DIR/bin + + + + + Compiling SAMtools requires the ncurses and zlib development libraries. + + + + + + JointSNVMix requires Python >= 2.7 + + + + + + + http://cython.org/release/Cython-0.19.1.tar.gz + $INSTALL_DIR/lib/python + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin + + $INSTALL_DIR/lib/python + $INSTALL_DIR/bin + + + + + + + + + + + http://pysam.googlecode.com/files/pysam-0.5.tar.gz + $INSTALL_DIR/lib/python + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin + + $INSTALL_DIR/lib/python + + + + + + + + + + http://joint-snv-mix.googlecode.com/files/JointSNVMix-0.7.5.tar.gz + $INSTALL_DIR/lib/python + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin + + $INSTALL_DIR/lib/python + $INSTALL_DIR/bin + + + + + + + + + +