NgsCctsBuildVelvet

Attention: Research Computing Documentation has Moved
https://docs.rc.uab.edu/

Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.

As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team

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

vi Makefile
/MAXKMER
$bcw57
LONGSEQUENCES=true
:wq

Build

make

done

NgsCctsBuildVelvet

Navigation menu

Search