From 279ac8d6c31e640ad7bb7d6809f3016a4497c887 Mon Sep 17 00:00:00 2001
From: Arun Seetharam <arnstrm@iastate.edu>
Date: Mon, 6 Jun 2016 11:46:55 -0500
Subject: [PATCH] Added a plant version of runBUSCO script as it needs a
 different busco script

---
 runBUSCO_genome.sh       | 16 ++++++++++------
 runBUSCO_plantgenomes.sh | 30 ++++++++++++++++++++++++++++++
 2 files changed, 40 insertions(+), 6 deletions(-)
 create mode 100755 runBUSCO_plantgenomes.sh

diff --git a/runBUSCO_genome.sh b/runBUSCO_genome.sh
index a1dfade..00b88a9 100755
--- a/runBUSCO_genome.sh
+++ b/runBUSCO_genome.sh
@@ -5,24 +5,28 @@
 # sh runBUSCO_genome.sh genome.fasta
 # Arun Seetharam
 # 2015/10/09 <arnstrm@iastate.edu>
-
-#+++++++++++++++++++++
-ORG=plantae
-#ORG=arthropoda
+#
+#####################################
+# DO NOT USE THIS FOR PLANT BUSCOS
+#####################################
+#
+#
+ORG=arthropoda
 #ORG=bacteria
 #ORG=eukaryota
 #ORG=fungi
 #ORG=metazoa
 #ORG=vertebrata
-#++++++++++++++++++++
 
 # (select one of the aboove)
 # results will be stored in the new directroy with the genome suffix
+
+
 module use /shared/software/GIF/modules
 module load busco/1.2
 genome="$1"
 outname=$(basename ${genome%.*})
-python3 ${BUSCO}/busco.py \
+python3 ${BUSCO_HOME}/busco.py \
   -o ${outname} \
   -in ${genome} \
   -l ${PROFILES}/${ORG} \
diff --git a/runBUSCO_plantgenomes.sh b/runBUSCO_plantgenomes.sh
new file mode 100755
index 0000000..541ee80
--- /dev/null
+++ b/runBUSCO_plantgenomes.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+# runs the busco pipeline on the genome assesment mode
+# if your genome is not plan change the select the suitable option below
+# run it as:
+# sh runBUSCO_genome.sh genome.fasta
+# Arun Seetharam
+# 2015/10/09 <arnstrm@iastate.edu>
+#
+#####################################
+# ONLY FOR PLANT BUSCOS
+#####################################
+#
+#
+ORG=plantae
+
+# (select one of the aboove)
+# results will be stored in the new directroy with the genome suffix
+
+
+module use /shared/software/GIF/modules
+module load busco/1.2_plants
+genome="$1"
+outname=$(basename ${genome%.*})
+python3 ${BUSCO_HOME}/busco.py \
+  -o ${outname} \
+  -in ${genome} \
+  -l ${PROFILES}/${ORG} \
+  -m all \
+  -c 16 \
+  -f