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smartdenovo-software [2019/03/21 19:38]
aorth created
smartdenovo-software [2019/04/10 06:37] (current)
aorth
Line 17: Line 17:
 Load one version into your environment and run it: Load one version into your environment and run it:
 <code>$ module load smartdenovo/git-5cc1356b <code>$ module load smartdenovo/git-5cc1356b
-$ smartdenovo.pl -p prefix -c 1 reads.fa > prefix.mak+$ smartdenovo.pl -p prefix -c 1 -t 4 reads.fa > prefix.mak
 $ make -f prefix.mak</code> $ make -f prefix.mak</code>
  
-See the [[https://github.com/ruanjue/smartdenovo/blob/master/README.md|README]] for more information.+Note that smartdenovo uses eight CPU threads by default, so please make sure to change that with the ''-t'' option and request the same number of CPUs in your [[https://hpc.ilri.cgiar.org/using-slurm#batch-jobs|SLURM batch job parameters]]. See the [[https://github.com/ruanjue/smartdenovo/blob/master/README.md|README]] for more information about the other command line options.
  
 ===== Installation ====== ===== Installation ======
smartdenovo-software.1553197138.txt.gz · Last modified: 2019/03/21 19:38 by aorth