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abyss-software

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Table of Contents

Abyss

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

Information

Usage

See versions of abyss which are available

module avail abyss

Installation

Notes from the sysadmin during installation:

cd /tmp
wget https://github.com/bcgsc/abyss/releases/download/1.5.2/abyss-1.5.2.tar.gz
tar xf abyss-1.5.2.tar.gz 
cd abyss-1.5.2
scl enable devtoolset-1.1 bash
mkdir /tmp/abyss-build
cd /tmp/abyss-build
LIBS="-lpthread" /tmp/abyss-1.5.2/configure --prefix=/export/apps/abyss/1.5.2 --with-boost=/export/apps/boost/1.50.0/include --with-mpi=/export/apps/openmpi/1.8.2
make -j4
sudo mkdir -p /export/apps/abyss/1.5.2
sudo chown aorth /export/apps/abyss/1.5.2
make install
sudo chown -R root:root /export/apps/abyss/1.5.2

Note: Seems to have a problem compiling with GCC 4.7.2 when you don't specify the extra LIBS. CentOS 6's 4.4.x works fine.

abyss-software.1409220716.txt.gz · Last modified: 2014/08/28 13:11 by aorth