Install from source

First of all, download the plantiSMASH python source from our GitHub repo:
https://github.com/plantismash/plantismash/releases

Then, make sure you have the following plantiSMASH dependencies installed:

• glimmer (version 3.02 tested)
• GlimmerHMM (version 3.0.4 tested)
• hmmer2 (version 2.3.2 tested, append a 2 to all hmmer2 executables to avoid conflict with hmmer3 executable names, like hmmalign -> hmmalign2)
• hmmer3 (version 3.0 and 3.1b2 tested)
• fasttree (version 2.1.7 tested)
• diamond (> 0.7.9 required, version 0.7.10 tested¹)
• muscle (version 3.8.31 tested)
• prodigal (version 2.6.1 tested)
• NCBI blast+ (version 2.2.31 tested)
• CD-HIT (version 4.6.6 tested)
• xz development headers (version 5.1.1 tested)
• xml development headers (version 2.9.1 tested)
• python (version 2.7 tested)
• pplacer (version 1.1 tested)
• GraPhlAn (version 1.1.3.1 tested)

Create virtual conda enviroment.for installing the plantiSMASH python dependencies.

mamba create -n plantismash python=2.7.18

Activate the conda environment.

conda activate plantismash

Install dependencies by runninginstall_dependencies.py :

python install_dependencies.py

Last but not least, run download_databases.py to grab and prepare the databases needed for the analyses:

python download_databases.py