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unicycler-software [2019/02/15 21:16]
aorth
unicycler-software [2020/01/21 12:38] (current)
jean-baka [Installation]
Line 32: Line 32:
 mkdir -p ${OUTDIR} mkdir -p ${OUTDIR}
  
-# run unicycler with the number of threads ​requested ​by SLURM+# 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} unicycler -t ${SLURM_NTASKS} -1 ${DATADIR}/​short_reads_1.fastq.gz -2 ${DATADIR}/​short_reads_2.fastq.gz -o ${OUTDIR}
  
Line 39: Line 39:
 echo echo
 echo " ​ ${OUTDIR}"</​code>​ 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 ======
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 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.1550254612.txt.gz · Last modified: 2019/02/15 21:16 by aorth