NgsCctsBuildAbyss

Abyss Cheaha Configuration Bash Command
./configure CPPFLAGS=-I/share/apps/ngs-ccts/include --enable-maxk=128 --with-boost=/share/apps/ngs-ccts/boost_1_49_0

Abyss Source Code Modification
Due to some compiler warnings about casting that were treated as errors on cheaha I applied the git patch detailed here: diff --git a/DistanceEst/DistanceEst.cpp b/DistanceEst/DistanceEst.cpp index 1c3c9ea..86fd0da 100644 --- a/DistanceEst/DistanceEst.cpp +++ b/DistanceEst/DistanceEst.cpp @@ -9,6 +9,7 @@ +#include @@ -138,7 +139,7 @@ static int estimateDistanceUsingMean(               unsigned& numPairs) {       Histogram h(samples.begin, samples.end); -      int d = pmf.mean - h.mean; +      int d = (int)round(pmf.mean - h.mean);
 * 1) include
 * 2) include
 * 3) include
 * 1) include
 * 2) include
 * 3) include 

// Count the number of samples that agree with the distribution. unsigned n = 0;

Older Information is Below:
Based on

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 ${TARGET2_VER} ./configure \ --with-boost=/share/apps/ngs-ccts/boost_1_49_0/boost \ --with-mpi=/usr/lib/openmpi \ CPPFLAGS=-I/share/apps/ngs-ccts/${TARGET_VAR}/include \ --enable-maxk=100 cd .. ln -fs ${TARGET2_VER} latest/abyss
 * 1) CPPFLAGS is for sparsehash
 * 1) link latest