added script

exercises/Pangenome_analysis/panaroo.sh

+#!/usr/bin/env bash
+#SBATCH --time=02:00:00
+#SBATCH --mem-per-cpu=20G
+#SBATCH --cpus-per-task=2
+#SBATCH --job-name=panaroo
+#SBATCH --output=panaroo_%j.out
+#SBATCH --error=panaroo_%j.err
+
+module load singularityce
+
+datadir=
+wd=
+singpath=/shares/amr.imm.uzh/bioinfo/singularity
+
+array=($(ls $datadir | cut -f 1 -d '_' | uniq))
+
+cd $wd
+mkdir -p panaroo/annotation_files
+mkdir -p panaroo/panaroo_output
+
+# gff file soft links
+for sample_id in "${array[@]}"
+do
+	ln -s $wd/$sample_id/prokka_annotation/$sample_id.gff $wd/panaroo/annotation_files/
+done 
+
+echo Starting panaroo $(date +"%T")
+cd panaroo
+$singpath/panaroo_1.3.0--pyhdfd78af_0.sif panaroo -i $wd/panaroo/annotation_files/*.gff -o ./panaroo_output/ --clean-mode strict --remove-invalid-genes
+echo Done $(date +"%T")
\ No newline at end of file