Package Recipe 'nerpa' — Bioconda documentation

recipe nerpa

A tool for discovering biosynthetic gene clusters of nonribosomal peptides.

Homepage:: gurevichlab/nerpa
Documentation:: gurevichlab/nerpa
License:: Dual-licensed under GPLv3 or CC BY-NC-SA 4.0
Recipe:: /nerpa/meta.yaml
Links:: doi: 10.1101/2024.11.19.624380v3, doi: 10.3390/metabo11100693, biotools: nerpa

Nerpa is a tool for linking biosynthetic gene clusters (BGCs) to known nonribosomal peptides (NRPs). BGCs are predicted in genome sequences (FASTA or GBK) with antiSMASH (Medema et al, 2011). Known NRPs are accepted in the SMILES format and processed with rBAN (Ricart et al, 2019).

package nerpa#

Versions:

2.1.0-1, 2.1.0-0, 1.0.0-7, 1.0.0-5, 1.0.0-4, 1.0.0-3, 1.0.0-2, 1.0.0-1, 1.0.0-0

Depends:

on _openmp_mutex >=4.5
on biopython
on bs4
on cairosvg
on dacite
on libgcc >=14
on libgomp
on libstdcxx >=14
on more-itertools
on networkx
on openjdk
on pandas >=1.5
on parse
on polars >=0.19
on prettytable
on pulp
on pyarrow
on python
on python-graphviz
on pyyaml
on rdkit
on requests
on scikit-learn 1.2.0

Additional platforms:

linux-aarch64, osx-arm64

Installation#

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi#

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install nerpa

to add into an existing workspace instead, run:

pixi add nerpa

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda#

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install nerpa

Alternatively, to install into a new environment, run:

conda create -n envname nerpa

with envname being the name of the desired environment.

Container#

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/nerpa:<tag>

(see nerpa/tags for valid values for <tag>).

Integrated deployment#

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

Link to this page#

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/nerpa/README.html)