eXpress

eXpress build instructions on TACC Ranger

eXpress instructions: http://bio.math.berkeley.edu/eXpress/tutorial.html#install
we don't need to install cmake or boost, already have that as a module
Setup environment
module swap pgi gcc
module load cmake
module load boost
Download source for eXpress and BamTools, both links are availabe in the above "intall" link
wget http://bio.math.berkeley.edu/eXpress/downloads/express-1.1.0/express-1.1.0-src.tgz
tar zxvf express-1.1.0-src.tgz
Download BamTools from githubhttps://github.com/pezmaster31/bamtools/tarball/master
extract BamTools into $EXPRESS_DIR then install
mkdir $EXPRESS_DIR/bamtools
tar zxvf pezmaster31-bamtools-6111130.tar.gz --transform="s/pezmaster31-bamtools-6111130/bamtools/"
cd bamtools
mkdir build
cd build
cmake ..
make
Build and Install eXpress
cd $EXPRESS_DIR
mkdir build
cd build
cmake ..
cmake doesn't do a good job of building the file "$EXPRESS_DIR/src/build/CMakeFile/express.dir/link.txt" it ignores the links needed for BamTools and Boost, but we can fix that!
echo "/opt/apps/gcc_amd/4.4.5/bin/c++ -I/opt/apps/gcc4_4/boost/1.48.0/include CMakeFiles/express.dir/biascorrection.o CMakeFiles/express.dir/bundles.o CMakeFiles/express.dir/fld.o CMakeFiles/express.dir/fragments.o CMakeFiles/express.dir/main.o CMakeFiles/express.dir/mapparser.o CMakeFiles/express.dir/markovmodel.o CMakeFiles/express.dir/mismatchmodel.o CMakeFiles/express.dir/robertsfilter.o CMakeFiles/express.dir/sequence.o CMakeFiles/express.dir/targets.o CMakeFiles/express.dir/threadsafety.o -o express -rdynamic -Wl,-rpath,/work/01863/benni/express-1.1.0-src/bamtools/lib -L/work/01863/benni/express-1.1.0-src/bamtools/lib -lbamtools -L/opt/apps/gcc4_4/boost/1.48.0/lib -lboost_filesystem -lboost_thread -lboost_system -lboost_program_options -lpthread" > $EXPRESS_DIR/src/build/CMakeFile/express.dir/link.txt
make CXX_FLAGS="-I$TACC_BOOST_INC -I../bamtools/inc"


		eXpress build instructions on TACC Ranger eXpress instructions: http://bio.math.berkeley.edu/eXpress/tutorial.html#install

we don't need to install cmake or boost, already have that as a module | |

	Setup environment
	module swap pgi gcc module load cmake module load boost
	Download source for eXpress and BamTools, both links are availabe in the above "intall" link
	wget http://bio.math.berkeley.edu/eXpress/downloads/express-1.1.0/express-1.1.0-src.tgz tar zxvf express-1.1.0-src.tgz
	Download BamTools from github
	https://github.com/pezmaster31/bamtools/tarball/master
	extract BamTools into $EXPRESS_DIR then install
	mkdir $EXPRESS_DIR/bamtools tar zxvf pezmaster31-bamtools-6111130.tar.gz --transform="s/pezmaster31-bamtools-6111130/bamtools/" cd bamtools mkdir build cd build cmake .. make
	Build and Install eXpress
	cd $EXPRESS_DIR mkdir build cd build cmake ..
		cmake doesn't do a good job of building the file "$EXPRESS_DIR/src/build/CMakeFile/express.dir/link.txt" it ignores the links needed for BamTools and Boost, but we can fix that!
	echo "/opt/apps/gcc_amd/4.4.5/bin/c++ -I/opt/apps/gcc4_4/boost/1.48.0/include CMakeFiles/express.dir/biascorrection.o CMakeFiles/express.dir/bundles.o CMakeFiles/express.dir/fld.o CMakeFiles/express.dir/fragments.o CMakeFiles/express.dir/main.o CMakeFiles/express.dir/mapparser.o CMakeFiles/express.dir/markovmodel.o CMakeFiles/express.dir/mismatchmodel.o CMakeFiles/express.dir/robertsfilter.o CMakeFiles/express.dir/sequence.o CMakeFiles/express.dir/targets.o CMakeFiles/express.dir/threadsafety.o -o express -rdynamic -Wl,-rpath,/work/01863/benni/express-1.1.0-src/bamtools/lib -L/work/01863/benni/express-1.1.0-src/bamtools/lib -lbamtools -L/opt/apps/gcc4_4/boost/1.48.0/lib -lboost_filesystem -lboost_thread -lboost_system -lboost_program_options -lpthread" > $EXPRESS_DIR/src/build/CMakeFile/express.dir/link.txt make CXX_FLAGS="-I$TACC_BOOST_INC -I../bamtools/inc"