eXpress build instructions on TACC Ranger
eXpress author's installation instructions: http://bio.math.berkeley.edu/eXpress/tutorial.html#install
On Ranger, 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
Setup environment:
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module swap $TACC_FAMILY_COMPILER gcc
module load cmake
module load boost
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Download source for eXpress and BamTools
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(both links are availabe in the
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author's installation instructions" link above)
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wget http://bio.math.berkeley.edu/eXpress/downloads/express-1.1.0/express-1.1.0-src.tgz |
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tar zxvf express-1.1.0-src.tgz |
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Setup environment
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Download source for eXpress and BamTools, both links are availabe in the above "intall" link
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Download BamTools from github
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https://github.com/pezmaster31/bamtools/tarball/master
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extract BamTools into $EXPRESS_DIR then install
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Build and Install eXpress
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cd ./express*/
# Remember where eXpress unpacked itself
MY_EXPRESS_DIR=`pwd`
# Download BamTools from github
wget --no-check-certificate https://github.com/downloads/pezmaster31/bamtools/bamtools-1.0.2.tar.gz
# extract BamTools into $MY_EXPRESS_DIR then install
tar zxvf bamtools-1.0.2.tar.gz
cd ./bamtools*/
# Remember where BamTools unpacked itself
MY_BAMTOOLS_DIR=`pwd`
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Build bamtools
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cd $MY_BAMTOOLS_DIR
mkdir build
cd build
cmake ..
make
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Build and Install eXpress
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cd $MY_EXPRESS_DIR
mkdir build
cd build
cmake ../src
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# cmake doesn't do a good job of building the file "$EXPRESS_DIR/src/build/CMakeFile/express.dir/link.txt" it ignores the links needed for BamTools and Boost, but we can fix that!
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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*/
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