eXpress

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:

module swap $TACC_FAMILY_COMPILER gcc
module load cmake
module load boost

Download source for eXpress and BamTools (both links are availabe in the "author's installation instructions" link above)

wget http://bio.math.berkeley.edu/eXpress/downloads/express-1.1.1/express-1.1.1-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`

Build bamtools

cd $MY_BAMTOOLS_DIR
mkdir build
cd build
cmake ..
make

Start building eXpress

cd $MY_EXPRESS_DIR/src
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX:PATH=$MY_EXPRESS_DIR ..

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!

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.

cp ./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 'NR==1{print $0;printf "-I%s\n",TACC_BOOST_INC};NR>1{print};/rdynamic/{exit};END{printf "-Wl,-rpath,%s/lib -L%s/lib -lbamtools %s/lib/libbamtools.a -L%s -lboost_filesystem -lboost_thread -lboost_system -lboost_program_options -lpthread\n",MY_BAMTOOLS_DIR,MY_BAMTOOLS_DIR,MY_BAMTOOLS_DIR,TACC_BOOST_LIB;}' | tr '\n' ' ' | xargs echo > ./CMakeFiles/express.dir/link.txt

Finish installing eXpress

make CXX_FLAGS="-I$TACC_BOOST_INC -I$MY_BAMTOOLS_DIR/include"
make install

This should put a binary executable called "express" in your $MY_EXPRESS_DIR/bin directory.