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h2. *eXpress build instructions on TACC Ranger |
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* author's installation instructions: [http://bio.math.berkeley.edu/eXpress/tutorial.html#install |
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] On Ranger, we don't need to install cmake or boost, already have that as a module |
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Setup |
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Setup environment:
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environment h5. *Setup environment:* {code} module swap $TACC_FAMILY_COMPILER gcc module load cmake module load boost |
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{code} h5. Download source for eXpress and BamTools (both links are availabe in the "author's installation instructions" link above) |
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{code} 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 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` |
Build bamtools
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{code} h5. Build bamtools {code} cd $MY_BAMTOOLS_DIR mkdir build cd build cmake .. make |
Build and Install eXpress
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{code} h5. Build and Install eXpress {code} cd $MY_EXPRESS_DIR mkdir build cd build cmake ../src {code} \# cmake doesn't do a good job of building the file "$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" > $EXPRESS_DIR/src/build/CMakeFile/express.dir/ |
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link.txt Edit: I want a way to edit this file, not just overwrite it. This is a work in progress: cat link.txt \| sed \-r "s/\s+/\n/g" \| awk \-v TACC_BOOST_INC=$TACC_BOOST_INC 'BEGIN {print "-I",TACC_BOOST_INC}; /rdynamic/ {exit}; {print}' {code} echo "`which 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" > $EXPRESS_DIR/src/build/CMakeFile/express.dir/link.txt {code} make CXX_FLAGS="-I$TACC_BOOST_INC \-I../bamtools*/include" |