From d71d75fa7a31a2cb2ec636b72897c5c99fda2677 Mon Sep 17 00:00:00 2001
From: Nikolaos Papadopoulos <npapadop@embl.de>
Date: Fri, 17 Jun 2022 10:57:17 +0200
Subject: [PATCH] was overeager during merging, restoring databases_pdb

---
 scripts/databases_pdb.sh | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100755 scripts/databases_pdb.sh

diff --git a/scripts/databases_pdb.sh b/scripts/databases_pdb.sh
new file mode 100755
index 0000000..5fafbd4
--- /dev/null
+++ b/scripts/databases_pdb.sh
@@ -0,0 +1,19 @@
+#!/bin/bash -ex
+#SBATCH -J create_index
+#SBATCH -t 08:00:00
+#SBATCH -c 64
+#SBATCH --mem=200G
+#SBATCH -o /g/arendt/npapadop/cluster/create_index.out
+#SBATCH -e /g/arendt/npapadop/cluster/create_index.err
+
+# build the indices for the sequence databases uniref30, PDB. This is later used for the
+# MSAs of the Spongilla sequences.
+
+cd /scratch/npapadop/database
+
+module load MMseqs2
+
+mmseqs databases PDB PDB tmp
+mmseqs createindex PDB tmp3 --remove-tmp-files 1 --threads 64
+
+module unload MMseqs2
-- 
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