NgsCctsBuildVelvet

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