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wget http://bio.math.berkeley.edu/eXpress/downloads/express-1.1.01/express-1.1.01-src.tgz tar zxvf express*.tgz cd ./express*/ # Remember where eXpress unpacked itself export 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 tar zxvf bamtools*.tar.gz # strip off the version number from the bamtools directory mv ./bamtools*/ ./bamtools/ cd ./bamtools export MY_BAMTOOLS_DIR=`pwd` |
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cd $MY_EXPRESS_DIR/src
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX:PATH=$MY_EXPRESS_DIR ..
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cmake doesn't do a good job of building the file "$EXPRESS_DIR/src/build/CMakeFile/express.dir/link.txt" it ignores the links needed for BamTools and Boost, but we can fix that!
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make CXX_FLAGS="-I$TACC_BOOST_INC -I$MY_BAMTOOLS_DIR/include"
make install
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This should put a binary executable called "express" in your $MY_EXPRESS_DIR/bin directory.