NgsCctsBuildVelvet

From UABgrid Documentation
(Difference between revisions)
Jump to: navigation, search
 
Line 12: Line 12:
 
  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 14:51, 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

Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox