Installing Gossamer bioinformatics suite in your $HOME
# add the needed environmental modules to your $HOME/.bashrc (if using csh/tcsh shell you will need to add similar commands to your $HOME/.cshrc or $HOME/.tcshrc files):
echo "module load gcc/4.9.3 > /dev/null 2>&1" >> $HOME/.bashrc
echo "module load zlib/1.2.11 > /dev/null 2>&1" >> $HOME/.bashrc
echo "module load cmake/3.7.2 > /dev/null 2>&1" >> $HOME/.bashrc
echo "module load intel/18.0.3 > /dev/null 2>&1" >> $HOME/.bashrc# request an interactive session:
qrsh ### wait for the interactive session to start
#cd $SCRATCH ### un-comment this instruction to build in $SCRATCH
git clone https://github.com/data61/gossamer.git
cd gossamer/
mkdir buildcd build# check that you have currently these modules loaded:
module li# should give you:
Currently Loaded Modulefiles:
1) ATS 2) gcc/4.9.3 3) intel/18.0.3 4) cmake/3.7.2 5) zlib/1.2.11# now issue
export BOOST_ROOT=/u/local/apps/boost/1_58_0/gcc-4.9.3
cmake -DCMAKE_INSTALL_PREFIX=$HOME/gossamer -DCMAKE_CXX_COMPILER=/u/local/compilers/gcc/4.9.3/bin/c++
-DZLIB_INCLUDE_DIR=/u/local/apps/zlib/1.2.11/intel-18.0.3_gcc-4.9.3/include
-DZLIB_LIBRARY_RELEASE=/u/local/apps/zlib/1.2.11/intel-18.0.3_gcc-4.9.3/lib/libz.so
..make
make installThe make step will take sometime, at the end of "make install" the executable will be in:
$HOME/gossamer/bin
to add them permanently to your $PATH you can issue:
echo "PATH=$HOME/gossamer/bin:$PATH" >> $HOME/.bashrc
. $HOME/.bashrc