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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

...

Setup environment:

module swap $TACC_FAMILY_COMPILER gcc
module load cmake
module load boost

...

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 
cdthe version number from the bamtools directory
mv ./bamtools*/ # Remember where BamTools unpacked itself
./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 ../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.

cp ./CMakeFiles/express.dir/

...

link.txt ./CMakeFiles/express.dir/

...

Edit: I want a way to edit this file, not just overwrite it.  This is a work in progress:

cat link.txt | 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 'BEGIN {-v MY_BAMTOOLS_DIR=$MY_BAMTOOLS_DIR 'NR==1{print $0;printf "-I%s\n","TACC_BOOST_INC"};NR>1{print}; /rdynamic/ {exit}; {print}'

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 END{printf "-Wl,-rpath,/work/01863/benni/express-1.1.0-src/bamtools/%s/lib -L/work/01863/benni/express-1.1.0-src/bamtools/L%s/lib -lbamtools -L%s/opt/apps/gcc4_4/boost/1.48.0/liblib/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 > $EXPRESS_DIR/src/build/CMakeFile./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.