From 3deed820eb997af886e1fe216ad4576785cc58fc Mon Sep 17 00:00:00 2001
From: Irene Ortega Sanz <irene.ortegasanz@ugent.be>
Date: Fri, 13 Dec 2024 10:07:42 +0100
Subject: [PATCH] Add 15_pangenome_roary.pbs

---
 scripts/15_pangenome_roary.pbs | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 scripts/15_pangenome_roary.pbs

diff --git a/scripts/15_pangenome_roary.pbs b/scripts/15_pangenome_roary.pbs
new file mode 100644
index 0000000..ab35811
--- /dev/null
+++ b/scripts/15_pangenome_roary.pbs
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+echo Start Job
+
+date
+
+
+mkdir ./SA/01_data_analysis/06_pangenome
+cd ./SA/01_data_analysis/06_pangenome
+
+mkdir input_files/
+
+echo Preparing gff input files from Prokka
+cp ./SA/01_data_analysis/04_annotation/*/*.gff input_files/
+
+module load Roary/3.13.0-foss-2020a
+
+echo Constructing pangenome using roary
+roary -p 32 -f . input_files/*.gff
+
+
+
+date
+
+echo End Job
\ No newline at end of file