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velvet [2017/10/03 21:14]
jokinsey created
velvet [2017/10/12 19:11]
jokinsey Fixed the job running location to /scratch/$PBS_JOBID
Line 26: Line 26:
 #!/bin/bash #!/bin/bash
 #PBS -N velvet #PBS -N velvet
 +#PBs -o velvet.$PBS_JOBID
 #PBS -l nodes=1:​ppn=12 #PBS -l nodes=1:​ppn=12
 #PBS -l walltime=00:​05:​00 #PBS -l walltime=00:​05:​00
Line 31: Line 32:
  
 cd $PBS_O_WORKDIR cd $PBS_O_WORKDIR
 +cp test_reads.fa /​scratch/​$PBS_JOBID
 +cd /​scratch/​$PBS_JOBID
  
 velveth velvet1 29 test_reads.fa velveth velvet1 29 test_reads.fa
 velvetg velvet1 velvetg velvet1
 +mv velvet1 $PBS_O_WORKDIR
 </​code>​ </​code>​
 +
 +This code will copy the test file to the ''/​scratch/​$PBS_JOBID''​ directory where we will be submitting the job from. Then the output will be in the directory ''​velvet1''​ which we move back to the directory we submitted the job from. Note that if you have already run the script you will have to remove the previous ''​velvet1''​ directory for the move command to work.
  
 All that remains is to submit the job. All that remains is to submit the job.
velvet.txt · Last modified: 2017/10/12 19:11 by jokinsey