Stacks 1.46

Dependencies

  • GNU GCC 5.4.0
  • SparseHash = 2.0.3

Installation

  1. First download the tar from the main page
$ wget http://catchenlab.life.illinois.edu/stacks/source/stacks-1.46.tar.gz
$ tar -zxvf stacks-1.46.tar.gz
  1. configure the makefile
cd stacks-1.46
module load gcc/5.4.0
sudo mkdir -p /share/apps/stacks/1.46/gcc-5.4.0
sudo chwon -R mgomezzul.apolo /share/apps/stacks/1.46/gcc-5.4.0
./configure --prefix=/share/apps/stacks/1.46/gcc-5.4.0 --build=redhat-linux-x86_64 CXXFLAGS="-O3 -march=native" CFLAGS="-O3 -march=native" CPPFLAGS="-O3 -march=native" --enable-sparsehash --with-sparsehash-include-path=/share/apps/sparsehash/2.0.3/gcc-5.4.0/include
make
make install
sudo chown -R root.root /share/apps/stacks/1.46/gcc-5.4.0

Module

#%Module1.0####################################################################
##
## module load stacks/1.46_gcc-5.4.0
##
## /share/apps/modules/stacks/1.46_gcc-5.4.0
##
## Written by Mateo Gómez-Zuluaga
##

proc ModulesHelp {} {
     global version modroot
     puts stderr "Sets the environment for using stacks 1.46\
         \n\in the shared directory \
         \n\t\t/share/apps/stacks/1.46/gcc-5.4.0\
         \n\t\tbuilded with gcc-5.4.0\
         \n\t\t"
}

module-whatis "(Name________)  stacks"
module-whatis "(Version_____)  1.46"
module-whatis "(Compilers___)  gcc-5.4.0"
module-whatis "(System______)  x86_64-redhat-linux"
module-whatis "(Libraries___)  sparsehash"

# for Tcl script use only
set         topdir        /share/apps/stacks/1.46/gcc-5.4.0
set         version       1.46
set         sys           x86_64-redhat-linux

conflict stacks

module load sparsehash/2.0.3_gcc-5.4.0

prepend-path PATH                $topdir/bin

Use mode

module load stacks/1.46_gcc-5.4.0

Author

  • Mateo Gómez-Zuluaga
  • Alejandro Salgado Gómez