====== Abyss ======
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler.

===== Information =====

  * Version: 2.1.4
  * Added: August, 2013
  * Updated: November, 2018
  * K-mer size: 128 (default at compile time)
  * Link: http://www.bcgsc.ca/platform/bioinfo/software/abyss

===== Usage =====

See versions of abyss which are available:
<code>$ module avail abyss</code>

Load one version into your environment and run it:
<code>$ module load abyss/2.1.4
$ abyss-pe help</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.1.4/abyss-2.1.4.tar.gz
$ tar xf abyss-2.1.4.tar.gz
$ cd abyss-2.1.4
$ sudo yum install sparsehash-devel.x86_64 openmpi3-devel.x86_64
$ export CPPFLAGS='-pthread -I/usr/include/openmpi3-x86_64'
$ export LIBS='-Wl,-rpath -Wl,/usr/lib64/openmpi3/lib -Wl,--enable-new-dtags -L/usr/lib64/openmpi3/lib -lmpi'
$ ./configure --prefix=/export/apps/abyss/2.1.4
$ make -j4
$ sudo mkdir -p /export/apps/abyss/2.1.4
$ sudo chown aorth /export/apps/abyss/2.1.4
$ make install
$ sudo chown -R root:root /export/apps/abyss/2.1.4
$ sudo yum remove sparsehash-devel.x86_64 openmpi3-devel.x86_64</code>

There is currently a [[https://github.com/bcgsc/abyss/issues/224|bug in configure's ability to detect the system's OpenMPI]] so we have to set the environment variables manually before building.