add scripts-download CENPK ChIPseq data

This commit includes the PBS scripts for downloading the CENPK ChIPseq data from Cai et al 2013 and updates the `.gitignore` file to include the FASTQ and log files.

Author: owlang

paper/.gitignore

@@ -35,3 +35,6 @@ SyntheticStrain/results/hg19*
 ENCODE_CellLines/results/BAM
 ENCODE_CellLines/results/BAM-nospike
 ENCODE_CellLines/results/ID
+CENPK-chipseq/logs/*.out-*
+CENPK-chipseq/logs/*.err-*
+CENPK-chipseq/results/FASTQ

paper/CENPK-chipseq/job/00_download_data.pbs

@@ -0,0 +1,22 @@
+#!/bin/bash
+#PBS -l nodes=1:ppn=8
+#PBS -l pmem=32gb
+#PBS -l walltime=06:00:00
+#PBS -A open
+#PBS -o logs/download.data.log.out
+#PBS -e logs/download.data.log.err
+
+# FIRST CHANGE PATH TO EXECUTE
+WRK=/path/to/GenoPipe/paper/CENPK-chipseq
+cd $WRK
+
+module load anaconda3
+source activate ~/work/myconda/genopipe/
+
+[ -d logs ] || mkdir logs
+[ -d results/FASTQ ] || mkdir -p results/FASTQ
+
+parallel-fastq-dump --gzip --split-files -t 8 -O results/FASTQ -s SRR518875
+parallel-fastq-dump --gzip --split-files -t 8 -O results/FASTQ -s SRR518876
+parallel-fastq-dump --gzip --split-files -t 8 -O results/FASTQ -s SRR518877
+parallel-fastq-dump --gzip --split-files -t 8 -O results/FASTQ -s SRR518878