NgsCctsBuildVelvet: Difference between revisions

Latest revision as of 19:51, 9 July 2013

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

@@ Line 1: / Line 1: @@
+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
@@ Line 6: / Line 12: @@
   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
@@ Line 17: / Line 23: @@
   make
+ or
+ make 'OPENMP=1' 'CATEGORIES=3' 'MAXKMERLENGTH=50'  (using commandline arguments)
 done