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Fixing issue #33

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This commit is contained in:
Sebastian Bassi 2024-04-29 10:09:33 -07:00
parent b461e12016
commit 86b6c4e881
3 changed files with 13 additions and 3 deletions
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10
README.md
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@ -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

4
input_prep/make_ss.sh
View file

@ -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.*

2
make_msa.sh
View file

@ -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