Add 15_pangenome_roary.pbs

ireneortega · Dec 13, 2024 · 3deed82 · 3deed82
1 parent ee014c2
commit 3deed82
Showing 1 changed file with 25 additions and 0 deletions.
diff --git a/scripts/15_pangenome_roary.pbs b/scripts/15_pangenome_roary.pbs
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+#!/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