NgsCctsBuildVelvet

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(Created page with " 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 c...")
 
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NOTE: it is possible to build Velvet to support > 1 threads: http://www.dolphing.com/re-velvet-users-velvet-1-1-01-multithreading-17
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* 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''
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* update galaxy/universe_wsgi.ini.sanitized to add -pe smp ''N''
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 +
Current build:
  
 
  TARGET_VER=velvet_1.2.08
 
  TARGET_VER=velvet_1.2.08

Revision as of 10:14, 4 April 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

vi Makefile
/MAXKMER
$bcw57
LONGSEQUENCES=true
:wq

Build

make

done

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