NgsCctsBuildAbyss

Based on [file:///share/apps/ngs-ccts/abyss-1.3.4/README.html#compilingabyssfromsource README.html:compiling from source]

Requires sparsehash

TARGET_VER=sparsehash-2.0.2
wget http://sparsehash.googlecode.com/files/${TARGET_VER}.tar.gz
tar xzvf ${TARGET_VER}.tar.gz
rm ${TARGET_VER}.tar.gz
cd ${TARGET_VER}
./configure --prefix=/share/apps/ngs-ccts/${TARGET_VER}
make
make install

Requires boost WARNING: boost seems to be on cheaha already - need to research more how to get abyss/configure to see it.

wget http://downloads.sourceforge.net/project/boost/boost/1.49.0/boost_1_49_0.tar.bz2
tar jxf boost_1_49_0.tar.bz2
(cd latest; ln -s boost_1_49_0/boost boost)

ABySS itself

TARGET2_VER=abyss-1.3.4
wget http://www.bcgsc.ca/downloads/abyss/${TARGET2_VER}.tar.gz
tar xzvf ${TARGET2_VER}.tar.gz
rm ${TARGET2_VER}.tar.gz
cd ${TARGET2_VER}
# CPPFLAGS is for sparsehash
./configure \
--with-boost=/share/apps/ngs-ccts/boost_1_49_0/boost \
--with-mpi=/usr/lib/openmpi \
CPPFLAGS=-I/share/apps/ngs-ccts/${TARGET_VAR}/include \
--enable-maxk=100
# link latest
cd ..
ln -fs ${TARGET2_VER} latest/abyss