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unicycler-software [2019/02/15 18:07]
aorth created
unicycler-software [2020/01/21 09:38] (current)
jean-baka [Installation]
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 ======
Line 37: Line 58:
  
 The devtoolset is used because Unicycler requires a GCC compiler newer than 4.9.1. The devtoolset is used because Unicycler requires a GCC compiler newer than 4.9.1.
 +
 +Note by JB: way after this install, on 21 Jan 2020, I had to change the header in /​export/​apps/​unicycler/​0.4.7/​bin/​unicycler from ''#​!/​usr/​bin/​python36''​ to ''#​!/​usr/​bin/​python3.6''​ because there is no (no longer?) python36 in ''​$PATH''​.
unicycler-software.1550254023.txt.gz · Last modified: 2019/02/15 18:07 by aorth