eXpress build instructions on TACC Ranger (in the bash shell)
author's installation instructions: http://bio.math.berkeley.edu/eXpress/tutorial.html#install
A few of these commands, like "export" are bash specific commands. Rather than make this installation guide a shell independent novel, I'll ask users to either translate those commands to your shell of choice or switch to bash (by typing bash at the command line) before proceeding.
On Ranger and Lonestar, we don't need to install cmake or boost, already have that as a module
Setup environment
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Setup environment:
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module swap $TACC_FAMILY_COMPILER gcc module load cmake module load boost |
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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-1.1.0-src.*.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 then install tar zxvf bamtools-1.0.2.*.tar.gz # strip off the version number from the cdbamtools directory mv ./bamtools*/ # Remember where BamTools unpacked itself ./bamtools/ cd ./bamtools export MY_BAMTOOLS_DIR=`pwd` |
Build bamtools
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cd $MY_BAMTOOLS_DIR mkdir build cd build cmake .. make |
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Start building eXpress
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cd $MY_EXPRESS_DIR/src mkdir build cd build cmake -DCMAKE_INSTALL_PREFIX:PATH=$MY_EXPRESS_DIR ../src |
# cmake doesn't do a good job of building the file "$EXPRESS_DIR/src/build/CMakeFile/express.dir/link.txt" it ignores the links needed for BamTools and Boost, but we can fix that! echo "/opt/apps/gcc_amd/4.4.5/bin/c++ -I/opt/apps/gcc4_4/boost/1.48.0/include
This little script is not the prettiest way to do this, but it works as a "cut and paste" way to add what is missing while reusing what we can to make this work on both Ranger and Lonestar. There's probably a better way to do this within cmake.
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cp ./CMakeFiles/express.dir/ |
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link.txt ./CMakeFiles/express.dir/ |
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link.txt.original cat ./CMakeFiles/express.dir/ |
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link.txt.original|sed -r "s/\s+/\n/g"|awk -v TACC_BOOST_INC=$TACC_BOOST_INC -v TACC_BOOST_LIB=$TACC_BOOST_LIB -v MY_BAMTOOLS_DIR=$MY_BAMTOOLS_DIR 'NR==1{print $0;printf "-I%s\n",TACC_BOOST_INC};NR>1{print};/rdynamic/{exit};END{printf "-Wl,-rpath, |
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%s/lib -L%s/lib -lbamtools %s/lib/libbamtools.a -L%s -lboost_filesystem -lboost_thread -lboost_system -lboost_program_options -lpthread |
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\n",MY_BAMTOOLS_DIR,MY_BAMTOOLS_DIR,MY_BAMTOOLS_DIR,TACC_BOOST_LIB;}' | tr '\n' ' ' | xargs echo > ./CMakeFiles/express.dir/link. |
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txt
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Finish installing eXpress
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make CXX_FLAGS="-I$TACC_BOOST_INC |
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-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.