(2022-06-27) Lab Notebook: AntiSMASH installation with Conda

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Lab Notebook --- Installing AntiSMASH on HPCC using Conda (2022-06-27)

AntiSMASH (The antibiotics & Secondary Metabolite Analysis Shell) is bioinformatics program for identifying genes belonging to secondary metabolite pathways, particularly in plant, fungi and bacteria species. Documentation for AntiSMASH can be found at https://docs.antismash.secondarymetabolites.org, but you will need to follow the instruction below to install AntiSMASH in your home directory on HPCC.

Small analyses can be done through their webportal (see https://docs.antismash.secondarymetabolites.org/website_submission/), however if your analysis requires running AntiSMASH on the HPCC, please see the instruction below for how to install this program localy using Anaconda

If you have not installed Anaconda in you home directory, see https://docs.icer.msu.edu/Using_conda/

Installing AnitSMASH

# Clear modules and load Anaconda
module purge
module load Conda/3

# Add biconda to your Anaconda install
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

# Create a cona environemnt for antimash and its depdencies
conda create -n antismash
conda activate antismash 

# As of version 6.1, you need to install each of these 
# programs first before install antismash or it never resolves
# Seems to be an issue with the conda recipie, not AntiSMASH itself
conda install hmmer2
conda install hmmer
conda install diamond
conda install fasttree
conda install prodigal
conda install blast
conda install muscle
conda install glimmerhmm

# Once the above installs have complete, this command will
# install antismash and update the versions of the above programs # as needed. 
# 
# You may be asked to 'DOWNGRADE' diamond, hmmer, muslce, 
# and some perl libraries; this is normal 
conda install antismash

# Test your install
antismash --check-prereqs
antismash --help

# Download databases
download-antismash-databases

Once you have completed the above steps, to run AntiSMASH in the future, do:

module purge
module load Conda/3

conda activate antismash

# check
antismash --help