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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

cd gossamer/
mkdir build

cd 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 install

The make step will take sometime, at the end of "make install" the executable will be in:


to add them permanently  to your $PATH you can issue:

echo "PATH=$HOME/gossamer/bin:$PATH" >> $HOME/.bashrc
. $HOME/.bashrc
Creation date: 12/5/2019 10:06 AM (dauria)      Updated: 12/5/2019 10:06 AM ()