Using Hostile on the HPC

Image

There is an image available for all QIB users:

singularity exec /qib/platforms/Informatics/transfer/outgoing/singularity/core/hostile__1.1.0.simg hostile --help

you can create an alias to simply run "hostile":

alias hostile='singularity exec /qib/platforms/Informatics/transfer/outgoing/singularity/core/hostile__1.1.0.simg hostile'

Databases

Databases are stored in

/qib/platforms/Informatics/transfer/outgoing/databases/hostile/

How to let hostile know?

export HOSTILE_CACHE_DIR=/qib/platforms/Informatics/transfer/outgoing/databases/hostile/

Running hostile

You can sbatch your job as you would normally do. Here here we use NBI::Slurm:

source package nbi-slurm
export hostile='singularity exec /qib/platforms/Informatics/transfer/outgoing/singularity/core/hostile__1.1.0.simg hostile'
export HOSTILE_CACHE_DIR=/qib/platforms/Informatics/transfer/outgoing/databases/hostile/
for FOR in reads/*_R1.fastq.gz;
do
  BASENAME=$(basename $FOR | cut -f1 -d_)
  REV=${FOR/_R1/_R2}
  runjob -q qib-medium -c 16 -m 64G -n hostile-$BASENAME \
     "HOSTILE_CACHE_DIR=/qib/platforms/Informatics/transfer/outgoing/databases/hostile/ $hostile \
     --fastq1 $FOR --fastq2 $REV --outdir clean-reads/ --threads 16"
done