ABySS

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Revision as of 08:57, 29 August 2013 by Rov (talk | contribs) (Created page with "ABySS is a denovo assembler of short read data. #/bin/sh #make and install abyss in my local directory #cd into abyss source distribution dir #and run this script using ../b...")
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ABySS is a denovo assembler of short read data.

  1. /bin/sh
  1. make and install abyss in my local directory
  2. cd into abyss source distribution dir
  3. and run this script using ../build_abyss.sh

load module openmpi

MYDIR="/ibers/ernie/home/rov/programs"

  1. boost does not need to be compiled

RJVBOOST="--with-boost=${MYDIR}/boost_1_54_0"

  1. found using find / 2> /dev/null | grep openmpi

RJVOPENMPI="--with-mpi=/cm/shared/apps/openmpi/gcc/64/1.4.4"

  1. see https://groups.google.com/forum/#!msg/abyss-users/6NXwP959RTI/tqLtO14a4A8J

RJVLDFLAGS="LDFLAGS=-L/cm/shared/apps/openmpi/gcc/64/1.4.4/lib64"

  1. probably only one of these required

RJVCPPFLAGS="-I${MYDIR}/sparsehash-2.0.2/src/google/sparsehash -I${MYDIR}/sparsehash-2.0.2/src/google -I${MYDIR}/sparsehash-2.0.2/src"

  1. where to put abyss binaries

RJVINSTALL="--prefix=${MYDIR}/abyss-local"

  1. ensure max kmer size is > 64

RJVMAXK='--enable-maxk=96'

./configure ${RJVINSTALL} ${RJVBOOST} ${RJVOPENMPI} ${RJVMAXK} ${RJVLDFLAGS} CPPFLAGS="${RJVCPPFLAGS}" make make install

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