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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 ===
-<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 "  ${OUTDIR}"</code>
+By default Unicycler will use four CPU threads. Please make sure to set this parameter properly according to the SLURM job request.
 ===== Installation ======
@@ Line 37: / Line 58: @@
 The devtoolset is used because Unicycler requires a GCC compiler newer than 4.9.1.
+Note by JB: way after this install, on 21 Jan 2020, I had to change the header in /export/apps/unicycler/0.4.7/bin/unicycler from ''#!/usr/bin/python36'' to ''#!/usr/bin/python3.6'' because there is no (no longer?) python36 in ''$PATH''.

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