NgsCctsBuildAbyss

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Attention: Research Computing Documentation has Moved
https://docs.rc.uab.edu/


Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.


As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team

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