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contributors:team_4_page [2015/06/01 07:32] emfeal |
contributors:team_4_page [2015/06/02 00:39] emfeal [Notes on Installation] |
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% --enable-dependency-tracking\ | % --enable-dependency-tracking\ | ||
% --with-boost=/campusdata/BME235/include/boost\ | % --with-boost=/campusdata/BME235/include/boost\ | ||
- | % --with-mpi=/campusdata/BME235/include\ | + | % --with-mpi=/opt/openmpi\ |
- | % CC=gcc-4.9.2 CXX=g++-4.9.2\ | + | % CC=gcc CXX=g++\ |
- | % CPPFLAGS=-I/campusdata/BME235/include/sparsehash | + | % CPPFLAGS=-I/campusdata/BME235/include/ |
</code> | </code> | ||
Then ABySS can be installed via the makefile | Then ABySS can be installed via the makefile | ||
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% make install | % make install | ||
</code> | </code> | ||
+ | ==== Notes on Installation ==== | ||
+ | * the //-enable-maxk// is by default set to 64. Always ensure the max kmer is set to the smallest possible value that accommodates your target kmers so as to minimize ABySS's memory footprint. | ||
+ | * ensure that the CPPFLAGS specified directory holds the google sparsehash includes. Look for a warning in the ABySS compilation to be sure. | ||
+ | * the boost libraries do not need to be compiled before installing. | ||
+ | * ensure openmpi is installed with the --with-sge option (for SGE) to ensure tight integration. | ||
=====ABySS parameters===== | =====ABySS parameters===== |