NgsCctsBuildVelvet: Difference between revisions
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cd ${TARGET_VER} | cd ${TARGET_VER} | ||
Edit Makefile to change max k mer available | Edit Makefile to change max k mer available or supply the values at the build time as commandline arguments. | ||
vi Makefile | vi Makefile | ||
| Line 23: | Line 23: | ||
make | make | ||
or | |||
make 'OPENMP=1' 'CATEGORIES=3' 'MAXKMERLENGTH=50' (using commandline arguments) | |||
done | done | ||
Latest revision as of 19:51, 9 July 2013
NOTE: it is possible to build Velvet to support > 1 threads: http://www.dolphing.com/re-velvet-users-velvet-1-1-01-multithreading-17
- add OPENMP=1 to Makefile (or 'OPENMP=1' argument to make)
- update galaxy/tools/sr_assembly/velvet*_wrapper.py to set OMP_NUM_THREADS=N-1 & OMP_THREAD_LIMIT=N-1
- update galaxy/universe_wsgi.ini.sanitized to add -pe smp N
Current build:
TARGET_VER=velvet_1.2.08 wget http://www.ebi.ac.uk/~zerbino/velvet/${TARGET_VER}.tgz tar xzvf ${TARGET_VER}.tgz rm ${TARGET_VER}.tgz cd ${TARGET_VER}
Edit Makefile to change max k mer available or supply the values at the build time as commandline arguments.
vi Makefile /MAXKMER $bcw57 LONGSEQUENCES=true :wq
Build
make or make 'OPENMP=1' 'CATEGORIES=3' 'MAXKMERLENGTH=50' (using commandline arguments)
done