NgsCctsBuildAbyss
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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