NgsCctsBuildAbyss

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(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...")
 
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

Revision as of 16:57, 9 October 2012

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 ${TARGET2_VER}
# CPPFLAGS is for sparsehash
./configure \
--with-boost=/share/apps/ngs-ccts/boost_1_49_0/boost \
--with-mpi=/usr/lib/openmpi \
CPPFLAGS=-I/share/apps/ngs-ccts/${TARGET_VAR}/include \
--enable-maxk=100
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