Creating a community around research computing at ILRI
@mralanorth
August 14, 2013
HUG Meetup #2
#!/bin/bash #SBATCH -p batch #SBATCH -J blastn #SBATCH -n 4 export BLASTDB=/export/data/bio/ncbi/blast/db module load blast/2.2.28+ blastn -query ~/data/sequences/drosoph_14_sequences.seq -db nt -num_threads 4
[aorth@hpc: ~]$ sbatch blastn.sh
#!/bin/bash POPULATIONS="1 2 3 4" REPS="1 2 3 4 5" STRUCTURE="/export/apps/structure/2.3.3/bin/structure" for rep in $REPS do for pop in $POPULATIONS do sbatch <<BATCH_SCRIPT #!/bin/bash #SBATCH -n 1 #SBATCH -p batch $STRUCTURE -e extraparams.txt -m mainparams.txt -K $pop -i pops_kenya.txt -o pops_kenya_K${pop}_rep${rep}.txt BATCH_SCRIPT done done
#!/bin/bash
POPULATIONS="1 2 3 4" REPS="1 2 3 4 5" STRUCTURE="/export/apps/structure/2.3.3/bin/structure" for rep in $REPS do for pop in $POPULATIONS do sbatch <<BATCH_SCRIPT #!/bin/bash #SBATCH -n 1 #SBATCH -p batch $STRUCTURE -e extraparams.txt -m mainparams.txt -K $pop -i pops_kenya.txt -o pops_kenya_K${pop}_rep${rep}.txt BATCH_SCRIPT done done
[aorth@hpc: ~]$ ./structure_batch.sh
By Alan Orth
A discussion of research computing facilities available at ILRI, including examples of how to use them!
GNU/Linux, coffee and death metal!