ABySS 2.2.3

Basic information

Installation

  1. Before compiling and installing ABySS install all its dependencies. After installing all the dependencies run:

    $ module load gcc/5.4.0
$ module load boost/1.67.0_intel-17.0.1
$ module load mvapich2/2.2.3a_gcc-5.4.0
$ module load sparsehash/2.0.3_intel-19.0.4
$ wget https://github.com/bcgsc/abyss/releases/download/2.2.3/abyss-2.2.3.tar.gz
$ tar xvf abyss-2.2.3.tar.gz
$ cd abyss-2.2.3
$ mkdir build && cd build
$ CFLAGS="-O3 -mavx2 -fopenmp" CXXFLAGS="-O3 -mavx2 -fopenmp" ../configure --prefix=/share/apps/abyss/2.2.3/gcc/5.4.0 --enable-mpich --with-mpi=/share/apps/mvapich2/2.2.3a/gcc-5.4.0
$ make -j10
$ make check

    Make sure all the tests passed. Then install it:

    $ sudo make install

  2. Create and place the needed module file. Create a file with the following content:

    2.2.3_gcc-5.4.0
    #%Module1.0####################################################################
##
## module load abyss/2.2.3_gcc-5.4.0
##
## /share/apps/modules/abyss/2.2.3_gcc-5.4.0
## Written by Vincent A. Arcila L and Hamilton Tobon Mosquera.
##

proc ModulesHelp {} {
         global version modroot
         puts stderr "Sets the environment for using abyss 2.2.3\
         \nin the shared directory /share/apps/abyss/2.2.3/gcc/5.4.0\
         \nbuilt with GCC 5.4.0."
}

module-whatis "(Name________) abyss"
module-whatis "(Version_____) 2.2.3"
module-whatis "(Compilers___) gcc-5.4.0"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) "

# for Tcl script use only
set         topdir        /share/apps/abyss/2.2.3/gcc/5.4.0
set         version       2.2.3
set         sys           x86_64-redhat-linux

conflict abyss
module load mvapich2/2.2.3a_gcc-5.4.0
module load arcs/1.1.0_gcc-7.4.0
module load tigmint/1.1.2_miniconda-4.5.1

prepend-path   PATH            $topdir/bin
prepend-path   MANPATH         $topdir/share/man

    Create the needed folder and place it:

    $ sudo mkdir /share/apps/modules/abyss
$ sudo mv 2.2.3_gcc-5.4.0 /share/apps/modules/abyss/

Authors