https://github.com/dzerbino/velvet/tree/master

Velvet je preveden s gcc 8 i parametrima:

module load gcc/8
make 'OPENMP=1'

Dostupne verzije su:

VerzijaModul
1.2.10velvet/1.2.10

Važno

Prilikom pokretanje aplikacije potrebno je definirati variablu "export OMP_NUM_THREADS=$NSLOTS" kako se posao nebi proširio po čitavom čvoru.

Primjer korištenja


module load velvet/1.2.10
velvetg --help
velveth --help

Test run


#!/bin/bash
#$ -N velvet
#$ -cwd
#$ -pe *mpi 4

module load velvet/1.2.10

export OMP_NUM_THREADS=$NSLOTS

velveth sillyDirectory 21 -shortPaired /apps/velvet/1.2.10/data/test_reads.fa
velvetg sillyDirectory
less sillyDirectory/stats.txt
velvetg sillyDirectory -cov_cutoff 5 -read_trkg yes -amos_file yes
less sillyDirectory/velvet_asm.afg
velvetg sillyDirectory -cov_cutoff auto
velvetg sillyDirectory -exp_cov 19 -ins_length 100
velvetg sillyDirectory -exp_cov auto
velveth sillyDirectory 21 -short /apps/velvet/1.2.10/data/test_reads.fa -long /apps/velvet/1.2.10/data/test_long.fa
velvetg sillyDirectory -exp_cov 19
velvetg sillyDirectory -exp_cov auto
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