add PBS script run StrainID on CENPK ChIPseq data

This commit includes a PBS script for running StrainID on the CENPK ChIPseq data from Cai et al 2013. The `.gitignore` file is also updated as appropriate.

Author: owlang

paper/.gitignore

@@ -39,3 +39,4 @@ CENPK-chipseq/logs/*.out
 CENPK-chipseq/logs/*.err
 CENPK-chipseq/results/FASTQ
 CENPK-chipseq/results/BAM
+CENPK-chipseq/results/ID

paper/CENPK-chipseq/job/02_run_StrainID.pbs

@@ -0,0 +1,27 @@
+#!/bin/bash
+#PBS -l nodes=1:ppn=4
+#PBS -l pmem=16gb
+#PBS -l walltime=03:00:00
+#PBS -A open
+#PBS -o logs/sid.cenpk.chip.log.out
+#PBS -e logs/sid.cenpk.chip.log.err
+
+# FIRST CHANGE PATH TO EXECUTE
+WRK=/path/to/GenoPipe/paper/CENPK-chipseq
+cd $WRK
+
+module load gcc
+module load samtools
+module load bwa
+module load anaconda3
+source activate ~/work/myconda/genopipe
+
+[ -d logs ] || mkdir logs
+[ -d results/ID ] || mkdir -p results/ID
+
+DB=$WRK/../db/sacCer3_VCF
+GENOME=$WRK/../input/sacCer3.fa
+
+STRAINID=$WRK/../../StrainID
+cd $STRAINID
+bash identify-Strain.sh -i $WRK/results/BAM -g $GENOME -o $WRK/results/ID/ -v $DB