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10 minute install

(not taking into account downloading and building the databases)

Assuming we are in a brand new Ubuntu instance

1 Update ubuntu

sudo apt-get update
sudo apt install gcc g++ make wget git

2 install usearch

Make sure you download VERSION 5.2.32!

I can't do anything else to help you here - you need to register and you will be sent a link by email.

link

Make sure the executable is in your PATH

3 download and install conda

(note if you already have a working, functioning install of conda, this step may be unnecessary)

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

# install it
sh Miniconda3-latest-Linux-x86_64.sh

# review license
# accept license
# accept or change home location
# yes to running conda init to place it in your path

# source .bashrc
source $HOME/.bashrc

# update conda (just because)
conda update -n base conda

4 clone this repo

git clone https://github.com/WatsonLab/MAGpy.git

5 create the main MAGpy environment

conda env create -f MAGpy/envs/install.yaml

# activate it
conda activate magpy_install

6 download data and build indices

# Uniprot - TREMBL
# NOTE - may require a large amount of RAM
wget -q ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz 
diamond makedb --in uniprot_trembl.fasta.gz -d uniprot_trembl
rm uniprot_trembl.fasta.gz

# Sourmash
wget -q https://s3-us-west-2.amazonaws.com/sourmash-databases/2018-03-29/genbank-d2-k31.tar.gz
gunzip < genbank-d2-k31.tar.gz | tar xvf -


# Pfam
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

# get checkM data
mkdir checkm_data
cd checkm_data
wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
gunzip < checkm_data_2015_01_16.tar.gz | tar xvf -
cd ..

7 update ete3 database

python MAGpy/scripts/update_ete3.py

NB there is currently an issue with ete3, see etetoolkit/ete#469

8 install phylophlan

hg clone https://bitbucket.org/nsegata/phylophlan

9 edit config.json

The file config.json tells MAGpy where everything is. On this installation on Ubuntu, it should (and does) look like this:

{
    "phylophlan_dir": "./phylophlan",
    "uniprot_sprot": "/home/ubuntu/uniprot_trembl",
    "sourmash_gbk": "/home/ubuntu/genbank-k31.sbt.json",
    "pfam_dir": "/home/ubuntu/",
    "checkm_dataroot": "./checkm_data"
}

10 make scripts executeable

chmod 755 MAGpy/scripts/*
chmod 755 MAGpy/test/scripts/*

11 Install Color::Mix

If you want to draw a tree of MAGs using GraPhlAn and our script "produce_tree.pl" then you will need to install Perl module "Color::Mix"

conda env create -f MAGpy/envs/basic2.yaml
source activate basic2

/usr/bin/env perl -MCPAN -e 'install Color::Mix'
# answer yes to automatic config