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 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
make install

The 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

cmake electus goss gossamer gossple xenome

Creation date: 12/5/2019 10:06 AM Updated: 12/5/2019 10:06 AM