# HG changeset patch # User Lance Parsons # Date 1347399923 14400 # Node ID 14bec14f4290d06505c26c3729c4cf3533318a37 # Parent f7a5b54a8d4f84c199fc1fc1fd1eb86f9bbc4ed6 Added tool_dependencies.xml back, dependency installation requires Galaxy changeset 7621:108cda898646 diff -r f7a5b54a8d4f -r 14bec14f4290 htseq-count.xml --- a/htseq-count.xml Mon Sep 10 17:30:10 2012 -0400 +++ b/htseq-count.xml Tue Sep 11 17:45:23 2012 -0400 @@ -2,6 +2,7 @@ - Count aligned reads in a BAM file that overlap features in a GFF file htseq-count -h | grep version | sed 's/^$.*$*$version .*$\./\2/' + numpy htseq samtools diff -r f7a5b54a8d4f -r 14bec14f4290 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Sep 11 17:45:23 2012 -0400 @@ -0,0 +1,58 @@ + + + + + + http://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.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://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.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 + + + + + Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package. + + + + + + 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. + + +