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1-dtool_create_0.sh
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#!/bin/bash -e
#SBATCH -p jic-short # partition (queue)
#SBATCH --mail-type=END,FAIL # notifications for job done & fail
#SBATCH --mail-user=jmoore@jic.ac.uk # send-to address
#SBATCH --array=
#SBATCH --mem=16000
#SBATCH -o 1-dtool_create_0.out
#SBATCH -e 1-dtool_create_0.err
until [ -f /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/0-wget_batch_0.txt ]; do
sleep 60
done
if [ ! -f /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/1-dtool_create_0.txt ]; then
cd /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets
#iinit
source /jic/scratch/groups/Daniel-Zilberman/load_dtool.sh
dtool create SRX2190716
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295279_1.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190716/data
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295279_2.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190716/data
dtool create SRX2190717
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295280.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190717/data
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295281.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190717/data
dtool create SRX2190718
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295282.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190718/data
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295283.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190718/data
dtool create SRX2190719
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295284.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190719/data
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295285.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190719/data
dtool create SRX2190720
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295286_1.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190720/data
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295286_2.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190720/data
dtool create SRX2190721
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295287_1.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190721/data
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295287_2.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190721/data
dtool create SRX2190722
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295288.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190722/data
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295289.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190722/data
dtool create SRX2190723
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295290_1.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190723/data
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295290_2.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190723/data
dtool create SRX2190724
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295291_1.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190724/data
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295291_2.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190724/data
dtool create SRX2190725
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295292_1.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190725/data
mv /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/SRR4295292_2.fastq.gz /jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/dtool_datasets/SRX2190725/data
echo complete>/jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/1-dtool_create_0.txt
echo 1-dtool_create_0 complete>>/jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/staging_log.txt
cd ..
sbatch 2-dtool_readme_0.sh
else
echo 1-dtool_create_0 already_complete>>/jic/scratch/groups/Daniel-Zilberman/Projects/Jay-1001_methylomes/0-raw_data/staging_log.txt
fi