NgsCctsBuildAbyss
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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.
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The Research Computing Team
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