Differences

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--- unicycler-software [2019/02/15 18:07] – created aorth
+++ unicycler-software [2023/06/12 13:17] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 0.47.0
+  * Version: 0.5.0
   * Added: February, 2019
+  * Updated: June, 2023
   * Link: https://github.com/rrwick/Unicycler
 ===== Usage =====
-See versions of unicycler which are available:
+See versions which are available:
 <code>$ module avail unicycler</code>
 Load one version into your environment and run it:
-<code>$ module load unicycler/0.47.0
+<code>$ module load unicycler/0.5.0
 $ unicycler</code>
 === Example Batch Job ===
-<code></code>
+<code>#!/usr/bin/env bash
+#SBATCH -p batch
+#SBATCH -n 4
+#SBATCH -J unicycler
+module load unicycler/0.5.0
+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 "  ${OUTDIR}"</code>
+By default Unicycler will use four CPU threads. Please make sure to set this parameter properly according to the SLURM job request.
 ===== Installation ======
@@ Line 25: / Line 47: @@
 <code>$ cd /tmp
-$ wget https://github.com/rrwick/Unicycler/archive/v0.4.7.zip
+$ wget https://github.com/rrwick/Unicycler/archive/refs/tags/v0.5.0.tar.gz
-$ unzip v0.4.7.zip
+$ tar xf v0.5.0.tar.gz
-$ cd Unicycler-0.4.7
+$ cd Unicycler-0.5.0
-$ sudo yum install centos-release-scl
+$ module load python/3.8
-$ sudo yum install devtoolset-6-gcc.x86_64 devtoolset-6-gcc-c++.x86_64 python36 python36-setuptools
+$ sudo mkdir -p /export/apps/unicycler/0.5.0
-$ scl enable devtoolset-6 bash
+$ sudo chown aorth /export/apps/unicycler/0.5.0
-$ sudo mkdir -p /export/apps/unicycler/0.4.7
+$ python3.8 setup.py install --prefix=/export/apps/unicycler/0.5.0
-$ sudo chown aorth /export/apps/unicycler/0.4.7
+$ sudo chown -R root:root /export/apps/unicycler/0.5.0</code>
-$ python36 setup.py install --prefix=/export/apps/unicycler/0.4.7
-$ sudo chown -R root:root /export/apps/unicycler/0.4.7</code>
-The devtoolset is used because Unicycler requires a GCC compiler newer than 4.9.1.