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 moduleSetup environment
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-1.1.0/express-1.1.0-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 $MY_EXPRESS_DIR then install tar zxvf bamtools-1.0.2.tar.gz cd ./bamtools*/ # Remember where BamTools unpacked itself export MY_BAMTOOLS_DIR=`pwd` |
Build bamtools
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mv ./CMakeFiles/express.dir/link.txt ./CMakeFiles/express.dir/link.txt.original;
cat ./CMakeFiles/express.dir/link.txt.original | sed -r "s/\s+/\n/g" | \
awk -v TACC_BOOST_INC=$TACC_BOOST_INC -v TACC_BOOST_LIB=$TACC_BOOST_LIB -v MY_BAMTOOLS_DIR=$MY_BAMTOOLS_DIR '
BEGIN {printf "-I%s\n",TACC_BOOST_INC};
{print}; /rdynamic/ {exit};
END {printf "-Wl,-rpath,%s/lib\n-L%s/lib\n-lbamtools\n-L%s -lboost_filesystem -lboost_thread -lboost_system -lboost_program_options -lpthread\n",MY_BAMTOOLS_DIR,MY_BAMTOOLS_DIR,TACC_BOOST_LIB;}' \
| tr '\n' ' ' | xargs echo > ./CMakeFiles/express.dir/link.txt
|
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make CXX_FLAGS="-I$TACC_BOOST_INC -I../bamtools*I$MY_BAMTOOLS_DIR/include" |