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Jellyfish is a k-mer counter.[1]

Picotte

Installed Version

Jellyfish 2.3.0 is installed on Picotte. Use the modulefile:

jellyfish/2.3.0 (NB will also load perl-threaded/5.32.1 and python/gcc/3.9.1)

Running Jellyfish

Jellyfish is multithreaded but does not support MPI. Request more than one CPU (i.e. CPU core) per task (one CPU per thread), e.g.

#SBATCH --nodes=1 #SBATCH --cpus-per-task=4

Proteus

Installed Versions

There are a few installed versions: 1.1.11, 2.1.3, and 2.2.10. The installed version 2.1.3 may be buggy as it did not pass all the tests in its accompanying test suite. The developer has been informed.

To use, load the appropriate module:

jellyfish/gcc/1.1.11 jellyfish/gcc/2.1.3 jellyfish/gcc/2.2.10  -- NB will also load perl-threaded/5.26.2 and python/3.6.1

Running Jellyfish

Jellyfish is multithreaded, and does not support MPI. Please use only the shm PE, e.g.

#$ -pe shm 4 jellyfish -t $NSLOTS ....

The -t option specifies the number of compute threads to run.

Please read the official documentation for details:

Compiling Jellyfish

INCOMPLETE

  • Download source from Github - https://github.com/gmarcais/Jellyfish
  • Use autotools to generate configure script
    • aclocal -I .
    • autoheader
    • automake --add-missing --copy --force-missing
    • autoconf
  • Modules

zlib/cloudflare/gcc/1.2.8 proteus-blas/gcc/64/20110419 proteus-lapack/gcc/64/3.5.0 gsl/gcc/2.2.1 samtools/1.8 perl-threaded/5.26.2 python/3.6.1

  • Environment variables:

HTSLIB_CFLAGS=-I/mnt/HA/opt/htslib/1.8/include HTSLIB_LIBS=-L/mnt/HA/opt/htslib/1.8/lib -Wl,-rpath,/mnt/HA/opt/htslib/1.8/lib -lhts SAMTOOLS=`which samtools`

  • configure

./configure --prefix=/mnt/HA/opt/jellyfish/gcc/2.2.10 --with-sse --enable-rpath \ --enable-htslib --disable-python-binding --enable-perl-binding --disable-ruby-binding

  • make
  • make check

References

[1] Jellyfish mer counter official website (formerly http://www.cbcb.umd.edu/software/jellyfish/)