User Tools

Site Tools


unicycler-software

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Next revision
Previous revision
Next revision Both sides next revision
unicycler-software [2019/02/15 18:07]
aorth created
unicycler-software [2019/02/15 18:36]
aorth
Line 19: Line 19:
 === Example Batch Job === === Example Batch Job ===
  
-<code></code>+<code>#!/usr/bin/env bash 
 +#SBATCH -p batch 
 +#SBATCH -n 4 
 +#SBATCH -J unicycler 
 + 
 +module load unicycler/0.4.7 
 + 
 +readonly DATADIR=~/sample_data 
 +readonly OUTDIR=/var/scratch/2019-02-15-aorth-unicycler 
 + 
 +# create output directory on compute node 
 +mkdir -p ${OUTDIR} 
 + 
 +# run unicycler with the number of threads allocated by SLURM 
 +unicycler -t ${SLURM_NTASKS} -1 ${DATADIR}/short_reads_1.fastq.gz -2 ${DATADIR}/short_reads_2.fastq.gz -o ${OUTDIR} 
 + 
 +echo 
 +echo "Remember to check (and clean!) output directory on ${SLURM_JOB_NODELIST}:" 
 +echo 
 +echo "  ${OUTDIR}"</code> 
 + 
 +By default Unicycler will use four CPU threads. Please make sure to set this parameter properly according to the SLURM job request.
  
 ===== Installation ====== ===== Installation ======
unicycler-software.txt · Last modified: 2020/01/21 09:38 by jean-baka