From 713d6f1a90bfc8cc365692482cc1e940da90c327 Mon Sep 17 00:00:00 2001
From: Alex Morehead <alex.morehead@gmail.com>
Date: Sun, 10 Mar 2024 14:47:31 -0500
Subject: [PATCH] Update make_msa.sh

---
 make_msa.sh | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/make_msa.sh b/make_msa.sh
index 9fbc874..0f59593 100755
--- a/make_msa.sh
+++ b/make_msa.sh
@@ -8,9 +8,12 @@ out_dir="$2"
 CPU="$3"
 MEM="$4"
 
-# pipe_dir
-PIPE_DIR="$5"
-DB_TEMPL="$6"
+# template database
+DB_TEMPL="$5"
+
+# current script directory (i.e., pipe directory)
+SCRIPT=`realpath -s $0`
+export PIPE_DIR=`dirname $SCRIPT`
 
 # sequence databases
 DB_UR30="$PIPE_DIR/uniclust/UniRef30_2021_06"