Purdue University

Commands

• CIRIquant

Module

You can load the modules by:

module load biocontainers
module load ciriquant

config.yml

All required dependencies have been installed within the CIRIquant container image. But users still need toprovide the PATH of these exectuables in `config.yml`. Please use the below `config.yml` as example:

name: hg38
tools:
   bwa: /bin/bwa
   hisat2: /bin/hisat2
   stringtie: /bin/stringtie
   samtools: /usr/local/bin/samtools
reference:
   fasta: reference/Homo_sapiens.GRCh38.dna.primary_assembly.fa
   gtf:  reference/Homo_sapiens.GRCh38.105.gtf
   bwa_index: reference/Homo_sapiens.GRCh38.dna.primary_assembly.fa
   hisat_index: reference/hg38_hisat2

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run CIRIquant on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 64
#SBATCH --job-name=ciriquant
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers ciriquant

CIRIquant -t 64 -1 SRR12095148_1.fastq -2 SRR12095148_2.fastq --config config.yml -o Output -p test