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PULpy

Open prediction of Polysaccharide Utilisation Loci (PUL)

Create conda env

conda env create -f envs/PULpy.yaml
source activate PULpy

Get Pfam data

# Pfam

mkdir pfam_data && cd pfam_data
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.dat.gz
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/active_site.dat.gz
gunzip Pfam-A.hmm.gz Pfam-A.hmm.dat.gz active_site.dat.gz
hmmpress Pfam-A.hmm
cd ..

Get DBCAN data

mkdir dbcan_data && cd dbcan_data
wget http://bcb.unl.edu/dbCAN2/download/Databases/dbCAN-old@UGA/hmmscan-parser.sh
wget http://bcb.unl.edu/dbCAN2/download/Databases/dbCAN-old@UGA/dbCAN-fam-HMMs.txt
hmmpress dbCAN-fam-HMMs.txt
chmod 755 hmmscan-parser.sh
cd ..

Edit config.json if you need to....

Make scripts executable

chmod -R 755 scripts

Input file

PULpy is designed to process genomes downloaded from NCBI, therefore expects them in a format:

"genomes/{id}_genomic.fna.gz")

That is, in a directory called "genomes", with a unique_id followed by "_genomic.fna.gz"

Run it

snakemake --use-conda