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smartdenovo-software [2019/03/21 22:38]
aorth created
smartdenovo-software [2019/04/10 09:37] (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.txt · Last modified: 2019/04/10 09:37 by aorth