Installation

Clone git repository

[ ]:

git clone https://github.com/labstructbioinf/pLAST.git
cd pLAST

conda / mamba environment

First, install the mamba environment using the core-env.yml file from the main pLAST repository:

mamba env create -n plast -f core-env.yml

You can also use conda:

conda env create -n plast -f core-env.yml

Alternatively, install the following dependencies manually:

hmmer >= 3.4
mmseqs2 >= 17.b804f
prodigal >= 2.6.3

Once all required packages are installed, activate the environment:
mamba activate plast
or
conda activate plast

If you plan to use Jupyter notebooks, install the ipykernel package as well:
mamba install ipykernel
or
conda install ipykernel

pip

[ ]:

pip install https://github.com/labstructbioinf/pLAST

Data download

Download models and metadata:

In notebooks directory create data dir.

[ ]:

mkdir -p data

[ ]:

wget -O data/59837579.tar.gz https://figshare.com/ndownloader/files/59837579 --user-agent="Mozilla/5.0"

--2025-11-25 19:01:50--  https://figshare.com/ndownloader/files/59837579
Resolving figshare.com (figshare.com)... 34.249.53.233, 54.77.166.26, 52.51.16.113, ...
Connecting to figshare.com (figshare.com)|34.249.53.233|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/59837579/data.tar.gz?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIYCQYOYV5JSSROOA/20251125/eu-west-1/s3/aws4_request&X-Amz-Date=20251125T180150Z&X-Amz-Expires=10&X-Amz-SignedHeaders=host&X-Amz-Signature=9afdb9a18aba85f5248143557d23d556ccc37082e6e5ca8c1ed475f06b6901d2 [following]
--2025-11-25 19:01:50--  https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/59837579/data.tar.gz?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIYCQYOYV5JSSROOA/20251125/eu-west-1/s3/aws4_request&X-Amz-Date=20251125T180150Z&X-Amz-Expires=10&X-Amz-SignedHeaders=host&X-Amz-Signature=9afdb9a18aba85f5248143557d23d556ccc37082e6e5ca8c1ed475f06b6901d2
Resolving s3-eu-west-1.amazonaws.com (s3-eu-west-1.amazonaws.com)... 3.5.66.135, 52.92.3.160, 3.5.71.39, ...
Connecting to s3-eu-west-1.amazonaws.com (s3-eu-west-1.amazonaws.com)|3.5.66.135|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 903680033 (862M) [application/gzip]
Saving to: ‘data/59837579.tar.gz’

data/59837579.tar.g 100%[===================>] 861.82M  6.35MB/s    in 2m 20s

2025-11-25 19:04:10 (6.14 MB/s) - ‘data/59837579.tar.gz’ saved [903680033/903680033]

[ ]:

tar -xzf data/59837579.tar.gz  && rm data/59837579.tar.gz

Download .hmm eggNOG database for eggnog models:

[ ]:

wget -O data/59861090.tar.gz https://figshare.com/ndownloader/files/59861090 --user-agent="Mozilla/5.0"

--2025-11-26 15:39:53--  https://figshare.com/ndownloader/files/59861090
Resolving figshare.com (figshare.com)... 34.246.58.166, 54.72.82.141, 54.220.91.93, ...
Connecting to figshare.com (figshare.com)|34.246.58.166|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/59861090/hmm_db.tar.gz?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIYCQYOYV5JSSROOA/20251126/eu-west-1/s3/aws4_request&X-Amz-Date=20251126T143953Z&X-Amz-Expires=10&X-Amz-SignedHeaders=host&X-Amz-Signature=824b7a1cd58049e8d6d9a7f659960cd11fcd3a6e87716f39889d0b23398089d0 [following]
--2025-11-26 15:39:53--  https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/59861090/hmm_db.tar.gz?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIYCQYOYV5JSSROOA/20251126/eu-west-1/s3/aws4_request&X-Amz-Date=20251126T143953Z&X-Amz-Expires=10&X-Amz-SignedHeaders=host&X-Amz-Signature=824b7a1cd58049e8d6d9a7f659960cd11fcd3a6e87716f39889d0b23398089d0
Resolving s3-eu-west-1.amazonaws.com (s3-eu-west-1.amazonaws.com)... 52.92.20.208, 3.5.66.27, 3.5.64.179, ...
Connecting to s3-eu-west-1.amazonaws.com (s3-eu-west-1.amazonaws.com)|52.92.20.208|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 8971867607 (8.4G) [application/gzip]
Saving to: ‘data/59861090.tar.gz’

data/59861090.tar.g 100%[===================>]   8.36G  6.23MB/s    in 23m 19s

2025-11-26 16:03:12 (6.12 MB/s) - ‘data/59861090.tar.gz’ saved [8971867607/8971867607]

[ ]:

tar -xzf data/59861090.tar.gz -C data && rm data/59861090.tar.gz

Go to basic pLAST usage:

https://labstructbioinf.github.io/pLAST/notebooks/usage.html