NgsCctsBuildAbyss

Abyss on Cheaha has been successfully installed (Dec 17th, 2012)

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 <algorithm>
 #include <cassert>
 #include <climits>
+#include <cmath>
 #include <cstdlib>
 #include <fstream>
 #include <getopt.h>
@@ -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());

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

Older Information is Below:

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