Package Recipe 'rsat-core' — Bioconda documentation

recipe rsat-core

Regulatory Sequence Analysis Tools (RSAT)

Homepage:: rsa-tools/rsat-code
Documentation:: http://rsat.eu
License:: AGPL / AGPL-3.0-only
Recipe:: /rsat-core/meta.yaml
Links:: biotools: rsat, doi: 10.1093/nar/gky317

Detection and analysis of regulatory signals in non-coding sequences.

package rsat-core#

Versions:

2026.10.08-0, 2025.04.04-1, 2025.04.04-0, 2020.02.29-1, 2020.02.29-0, 2020.02.28-0, 2020.01.04-0

Depends:

on bioconductor-qvalue
on d3
on ghostscript
on httplib2
on libgcc >=14
on libgfortran
on libgfortran5 >=14.4.0
on libpq
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on matplotlib-base
on numpy
on opencv
on openssl
on perl
on perl-algorithm-cluster
on perl-app-cpanminus
on perl-bio-das
on perl-cgi
on perl-class-std-fast
on perl-data-dumper
on perl-db_file
on perl-dbd-mysql
on perl-dbi
on perl-email-simple
on perl-ensembl-genomes
on perl-file-spec
on perl-http-tiny
on perl-io-all
on perl-json
on perl-libwww-perl
on perl-lockfile-simple
on perl-log-log4perl
on perl-lwp-simple
on perl-math-cdf
on perl-mce-shared
on perl-net-http >=6.18
on perl-net-ssleay
on perl-number-format
on perl-object-insideout
on perl-parallel-forkmanager
on perl-posix
on perl-postscript-simple
on perl-readonly
on perl-statistics-distributions
on perl-xml-parser
on perl-yaml
on pygraphviz
on python
on pyyaml
on r-base
on r-data.table
on r-dendextend
on r-dplyr
on r-dynamictreecut
on r-egg
on r-flux
on r-ggplot2
on r-gplots
on r-gridextra
on r-jpeg
on r-png
on r-rcolorbrewer
on r-reshape2
on r-rjsonio
on r-zoo
on scipy
on seqlogo
on snakemake >=7.0
on weblogo
on zlib >=1.3.1,<2.0a0

Additional platforms:

linux-aarch64

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 rsat-core

to add into an existing workspace instead, run:

pixi add rsat-core

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 rsat-core

Alternatively, to install into a new environment, run:

conda create -n envname rsat-core

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/rsat-core:<tag>

(see rsat-core/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.

Notes#

This package installs RSAT tools to analyse cis-regulatory elements, supporting: * motif discovery (support genome-wide data sets like ChIP-seq) * transcription factor binding motif analysis (quality assessment, comparisons and clustering) * comparative genomics * analysis of regulatory variations

Documentation can be found at https://rsa-tools.github.io/installing-RSAT

Note that this package does not include genome sequences nor DNA motif collections, please check https://rsa-tools.github.io/installing-RSAT/RSAT-Docker/RSAT-Docker-tuto.html to learn how to add them in your system.

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/rsat-core/README.html)