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input.txt
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input.txt
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# For this input script to work, you have to keep comments to a single line. this script should contain various parameters you can set for your RNA-seq job. each parameter follows a comment describing what it refers to.
# working directory
/work/m/maxwell9/
# email to send output to
# sample directory
/shares/biocomputing_i/FASTQ_Files/test2
# gff file
/shares/biocomputing_i/FASTQ_Files/test2/genes.gff
# genome reference
/shares/biocomputing_i/FASTQ_Files/test2/genome.fa
# number of CPU cores to request. Since we're using the slurm array, only 2 reads run on this number of CPUs, so don't need as many CPUs.
2
# amount of memory to request for Tophat in megabytes. this is the value of x in #SBATCH --mem=x.
10000
# number of hours the main script will take. must be < 2 hrs to run on dev partition.
1
# number of minutes the main script will take after the hours above have completed. must be < 60. for example if you wanted to schedule 5 hours and 15 minutes, you would put 5 in the line above and 15 in the line below.
55