Merge pull request #100 from ToyokoLabs/bugfix33

Fixing error ERROR: could not open file '.../RoseTTAFold-All-Atom/uniclust/UniRef30_2021_06_cs219.ffdata'

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
 

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.*
+rm $ID.*

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