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Commit e3dbb9f3 authored by Laura Cook's avatar Laura Cook
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#!/bin/bash
### Author: Laura E Cook, University of Melbourne, 22/01/2020
### Last update: 07/02/2020
### Purpose: basic array wrapper script
# Array set up:
#SBATCH --array=618-718
# Partition for the job:
# The project ID which this job should run under:
#SBATCH -A punim0586
# Maximum number of tasks/CPU cores used by the job:
#SBATCH --mem=50000
#SBATCH --partition mig
# Send yourself an email when the job:
# aborts abnormally (fails)
#SBATCH --mail-type=FAIL
# ends successfully
#SBATCH --mail-type=END
#SBATCH --mail-user=lecook@student.unimelb.edu.au
# The maximum running time of the job in days-hours:mins:sec
#SBATCH --time=50:00:00
# The name of the job:
#SBATCH --job-name=array
# Output control:
#SBATCH --error="/data/projects/punim0586/lecook/chipseq-pipeline/cross_species/logs/lastz_%a.stderr"
#SBATCH --output="/data/projects/punim0586/lecook/chipseq-pipeline/cross_species/logs/lastz_%a.stdout"
# Load modules:
module load foss
module load lastz
conda activate wga
# Run the simulations:
command=`head -n $SLURM_ARRAY_TASK_ID /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/scripts/lastz_commands.sh | tail -n 1`
echo "SLURM_ARRAY_TASK_ID: " $SLURM_ARRAY_TASK_ID
echo $command
eval $command
\ No newline at end of file
##!/usr/bin/env bash
## Change file names in a loop
TRA=($(for file in *.fa.masked; do echo $file |cut -d "." -f 1;done))
echo ${TRA[@]}
for tr in ${TRA[@]};
do
mv ${tr}.fa.masked ${tr}.fa
done
\ No newline at end of file
......@@ -12,6 +12,6 @@ for tr in ${TRA[@]};
do
echo 'lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/pun$
echo 'lastz_32 /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/mm10.fa[multiple] /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/smiCra1_RM/'${tr}.fa 'H=2000 K=2400 L=3000 Y=9400 --format=maf > /data/projects/punim0586/lecook/chipseq-pipeline/cross_species/data/genomes/maf/'${tr}_mm10.smiCra1.maf
done
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