using-slurm
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using-slurm [2013/12/02 14:04] – [Using SLURM] aorth | using-slurm [2013/12/02 14:21] – aorth | ||
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* highmem | * highmem | ||
- | " | + | " |
To see more information about the queue configuration, | To see more information about the queue configuration, | ||
Line 26: | Line 26: | ||
#SBATCH -n 4 | #SBATCH -n 4 | ||
- | export BLASTDB=/ | + | # load the blast module |
module load blast/ | module load blast/ | ||
+ | # run the blast with 4 CPU threads (cores) | ||
blastn -query ~/ | blastn -query ~/ | ||
Line 37: | Line 37: | ||
==== Batch job using local storage ==== | ==== Batch job using local storage ==== | ||
- | Users' home directories | + | Users' home folders |
Instead, you can use a local " | Instead, you can use a local " | ||
Line 44: | Line 44: | ||
#SBATCH -p batch | #SBATCH -p batch | ||
#SBATCH -n 4 | #SBATCH -n 4 | ||
- | #SBATCH -J test | + | #SBATCH -J blastn |
+ | |||
+ | # load the blast module | ||
+ | module load blast/ | ||
WORKDIR=/ | WORKDIR=/ | ||
Line 52: | Line 55: | ||
echo | echo | ||
- | Trinity.pl --seqType fq --JM 10G --single AR1960BN.fastq --output | + | # run the blast with 4 CPU threads (cores) |
+ | blastn -query ~/ | ||
All output is directed to '' | All output is directed to '' | ||
+ | |||
==== Check queue status ==== | ==== Check queue status ==== | ||
< | < |
using-slurm.txt · Last modified: 2022/11/03 11:38 by jean-baka