dark_matter/submit_dark_matter.pbs at master · developing-bioinformatics/dark_matter · GitHub

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#!/bin/bash -l
#
#Number of cores requested
#$ -pe omp 16

#Give the name to the job
#$ -N dark_matter

#Output file destination
#$ -o outputs/$JOB_NAME.o$JOB_ID

#Send an email when the job is finished (or aborted)
#$ -M enpederson@gmail.com
#$ -m ae


#Join the error and output file
#$ -j y


# Set the runtime limit (default 16 hours):
#$ -l h_rt=18:00:00

# Specify your project
#$ -P ct-shbioinf


# Stuff to execute:

module load blast+ #load blast module
#module load sratoolkit
module load R/3.6.2 #load R3.6.2

cd /projectnb/ct-shbioinf/epederso/dark_matter/ #use your notes or project folder. Wherever your script is located

#srr_list = ("SRR11043467","SRR11043468","SRR11043469","SRR11043470","SRR11043471",
#             "SRR11043472","SRR11043473","SRR11043474","SRR11043475","SRR11043476",
#             "SRR11043477","SRR11043478","SRR11043479","SRR11043480","SRR11043481",
#             "SRR11043482","SRR11043483","SRR11043484","SRR11043486","SRR11043487",
#             "SRR11043488","SRR11043489","SRR11043490","SRR11043491","SRR11043493",
#             "SRR11043494","SRR11043495","SRR11043496","SRR11043497","SRR11043498",
#             "SRR11043499","SRR11043500","SRR11043501","SRR11043502","SRR11043503",
#             "SRR11043504","SRR11043505","SRR11043506","SRR11043507","SRR11043508",
#             "SRR11043509","SRR11043510","SRR11043511","SRR11043512","SRR11043513",
#             "SRR11043514","SRR11043515","SRR11043516","SRR11043517","SRR11043492",
#             "SRR11206993","SRR11206994","SRR11206995","SRR11206996","SRR11206997",
#             "SRR11206998","SRR11206999","SRR11043485")

echo "SRR11043496"

Rscript 'code/run_dark_matter_PBS.R' #run the scripts