install.sh

#!/bin/bash

# get the scripts path
SCRIPT=`realpath -s $0`
SCRIPTPATH=`dirname $SCRIPT`

# build a new environment
conda create -y -n poem_py3 python=3

eval "$(conda shell.bash hook)"
conda activate poem_py3 
# install third part software and packages:
conda install -y -c bioconda diamond prokka=1.12 idba cd-hit keras=2.2.4 networkx biopython numpy art 

conda install -y -c biobuilds perl=5.22

# download the cog2014 database.
echo "Download COG database"
wget -q -c ftp://ftp.ncbi.nih.gov/pub/COG/COG2014/data/*2014* -P $SCRIPTPATH/database/cog/cog2014

# unzip cog fasta file and format
echo "Unzip cog fasta and format the file by diamond"
gunzip $SCRIPTPATH/database/cog/cog2014/prot2003-2014.fa.gz
diamond makedb --in $SCRIPTPATH/database/cog/cog2014/prot2003-2014.fa -d $SCRIPTPATH/database/cog/cog2014/prot2003-2014.fa


conda deactivate