NgsCctsBuildAbyss - Revision history

Ozborn@uab.edu: Notes on sucessfull compiling of abyss

2012-12-17T21:17:21Z

Notes on sucessfull compiling of abyss

← Older revision		Revision as of 21:17, 17 December 2012
Line 1:		Line 1:
			==Abyss on Cheaha has been successfully installed (Dec 17th, 2012)==

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

			=== 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:
			<pre>
			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;
			</pre>

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

Curtish@uab.edu at 22:05, 9 October 2012

2012-10-09T22:05:11Z

← Older revision		Revision as of 22:05, 9 October 2012
Line 14:		Line 14:

	Requires [http://sourceforge.net/projects/boost/ boost]		Requires [http://sourceforge.net/projects/boost/ boost]
	<big>WARNING</big>: boost seems to be on cheaha already - need to research more how to get abyss/configure to see it.		<big>'''WARNING'''</big>: 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		wget http://downloads.sourceforge.net/project/boost/boost/1.49.0/boost_1_49_0.tar.bz2

Curtish@uab.edu at 22:04, 9 October 2012

2012-10-09T22:04:45Z

← Older revision		Revision as of 22:04, 9 October 2012
Line 14:		Line 14:

	Requires [http://sourceforge.net/projects/boost/ boost]		Requires [http://sourceforge.net/projects/boost/ boost]
			<big>WARNING</big>: 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		wget http://downloads.sourceforge.net/project/boost/boost/1.49.0/boost_1_49_0.tar.bz2

Curtish@uab.edu at 22:03, 9 October 2012

2012-10-09T22:03:56Z

← Older revision		Revision as of 22:03, 9 October 2012
Line 17:		Line 17:
	wget http://downloads.sourceforge.net/project/boost/boost/1.49.0/boost_1_49_0.tar.bz2		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		tar jxf boost_1_49_0.tar.bz2
	ln -s boost_1_49_0/boost boost		(cd latest; ln -s boost_1_49_0/boost boost)

	ABySS itself		ABySS itself

Curtish@uab.edu at 21:58, 9 October 2012

2012-10-09T21:58:54Z

← Older revision		Revision as of 21:58, 9 October 2012
Line 32:		Line 32:
	CPPFLAGS=-I/share/apps/ngs-ccts/${TARGET_VAR}/include \		CPPFLAGS=-I/share/apps/ngs-ccts/${TARGET_VAR}/include \
	--enable-maxk=100		--enable-maxk=100
			# link latest
			cd ..
			ln -fs ${TARGET2_VER} latest/abyss

Curtish@uab.edu at 21:57, 9 October 2012

2012-10-09T21:57:02Z

← Older revision		Revision as of 21:57, 9 October 2012
Line 2:		Line 2:
	Based on [file:///share/apps/ngs-ccts/abyss-1.3.4/README.html#compilingabyssfromsource README.html:compiling from source]		Based on [file:///share/apps/ngs-ccts/abyss-1.3.4/README.html#compilingabyssfromsource README.html:compiling from source]

	Requires [sparsehash]		Requires [http://code.google.com/p/sparsehash sparsehash]

	TARGET_VER=sparsehash-2.0.2		TARGET_VER=sparsehash-2.0.2
Line 13:		Line 13:
	make install		make install

	Requires [boost]		Requires [http://sourceforge.net/projects/boost/ boost]

	wget http://downloads.sourceforge.net/project/boost/boost/1.49.0/boost_1_49_0.tar.bz2		wget http://downloads.sourceforge.net/project/boost/boost/1.49.0/boost_1_49_0.tar.bz2
Line 28:		Line 28:
	# CPPFLAGS is for sparsehash		# CPPFLAGS is for sparsehash
	./configure \		./configure \
	--with-boost=/~~usr~~/~~local~~/~~include~~ \		--with-boost=/share/apps/ngs-ccts/boost_1_49_0/boost \
	--with-mpi=/usr/lib/openmpi \		--with-mpi=/usr/lib/openmpi \
	CPPFLAGS=-I/share/apps/ngs-ccts/${TARGET_VAR}/include \		CPPFLAGS=-I/share/apps/ngs-ccts/${TARGET_VAR}/include \
	--enable-maxk=100		--enable-maxk=100

Curtish@uab.edu: Created page with " 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..."

2012-10-09T21:52:35Z

Created page with " 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..."

New page

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]

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
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 ${TARGET2_VER}
# CPPFLAGS is for sparsehash
./configure \
--with-boost=/usr/local/include \
--with-mpi=/usr/lib/openmpi \
CPPFLAGS=-I/share/apps/ngs-ccts/${TARGET_VAR}/include \
--enable-maxk=100