Log into Puhti using your CSC credentials.
Move to the course project scatch directory and make a subdirectory for yourself
cd /scratch/project_xxxx
mkdir $USER
cd $USER
mkdir trinity
cd trinity
In this exercise we use ready provided Singularity image and data to keep things simple.
Make and save the following batch job script as e.g. trinity.sh
#!/bin/bash
#SBATCH --time=00:30:00
#SBATCH --partition=small
#SBATCH --account=project_xxxx
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=5
#SBATCH --mem=4000
export TMPDIR=$PWD
singularity exec --bind $PWD:$PWD --bind /scratch/project_xxx/Trinity:/data /scratch/project_xxx/Trinity/trinityrnaseq_latest.sif \
Trinity --seqType fq \
--max_memory 1G \
--CPU 5 \
--output $PWD/TrinityOut \
--left /data/reads.left.fq.gz \
--right /data/reads.right.fq.gz \
Submit the job:
sbatch trinity.sh