From 86b6c4e8812e0567cc9893a905b90965ac3b86b2 Mon Sep 17 00:00:00 2001
From: Sebastian Bassi <sebastian@toyoko.io>
Date: Mon, 29 Apr 2024 10:09:33 -0700
Subject: [PATCH] Fixing issue #33

---
 README.md             | 10 +++++++++-
 input_prep/make_ss.sh |  4 +++-
 make_msa.sh           |  2 +-
 3 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 7d071ab..6fe5fc5 100644
--- a/README.md
+++ b/README.md
@@ -74,7 +74,15 @@ tar xfz bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz -C ./bfd
 wget https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz
 tar xfz pdb100_2021Mar03.tar.gz
 ```
-
+8. Download BLAST
+```
+wget https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz
+mkdir -p blast-2.2.26
+tar -xf blast-2.2.26-x64-linux.tar.gz -C blast-2.2.26
+cp -r blast-2.2.26/blast-2.2.26/ blast-2.2.26_bk
+rm -r blast-2.2.26
+mv blast-2.2.26_bk/ blast-2.2.26
+```
 <a id="inference-config"></a>
 ### Inference Configs Using Hydra
 
diff --git a/input_prep/make_ss.sh b/input_prep/make_ss.sh
index bb792f4..2ddc214 100644
--- a/input_prep/make_ss.sh
+++ b/input_prep/make_ss.sh
@@ -1,6 +1,8 @@
 #!/bin/bash
 # From: https://github.com/RosettaCommons/RoseTTAFold
 
+export BLASTMAT=$PIPE_DIR/blast-2.2.26/data/
+
 DATADIR="$CONDA_PREFIX/share/psipred_4.01/data"
 echo $DATADIR
 
@@ -27,4 +29,4 @@ grep "^Conf" $ID.horiz | awk '{print $2}'
 ) | awk '{if(substr($1,1,1)==">") {print "\n"$1} else {printf "%s", $1}} END {print ""}' | sed "1d" > $o_ss
 
 rm ${i_a3m}.csb.hhblits.ss2
-rm $ID.*
\ No newline at end of file
+rm $ID.*
diff --git a/make_msa.sh b/make_msa.sh
index 6da7bc4..4a3c98c 100755
--- a/make_msa.sh
+++ b/make_msa.sh
@@ -16,7 +16,7 @@ SCRIPT=`realpath -s $0`
 export PIPE_DIR=`dirname $SCRIPT`
 
 # sequence databases
-DB_UR30="$PIPE_DIR/uniclust/UniRef30_2021_06"
+DB_UR30="$PIPE_DIR/UniRef30_2020_06/UniRef30_2020_06"
 DB_BFD="$PIPE_DIR/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt"
 
 # Running signalP 6.0