recipe rsat-core

Regulatory Sequence Analysis Tools (RSAT)

Homepage:

http://rsat.eu

License:

GNU Affero General Public License v3

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:

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 bioconductor-qvalue:

depends d3:

depends ghostscript:

depends httplib2:

depends libgcc:

>=13

depends libgfortran:

depends libgfortran5:

>=13.4.0

depends libpq:

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends matplotlib-base:

depends numpy:

depends opencv:

depends openssl:

3.5.4.*

depends perl:

depends perl-algorithm-cluster:

depends perl-app-cpanminus:

depends perl-bio-das:

depends perl-cgi:

depends perl-class-std-fast:

depends perl-data-dumper:

depends perl-db_file:

depends perl-dbd-mysql:

depends perl-dbi:

depends perl-email-simple:

depends perl-ensembl-genomes:

depends perl-file-spec:

depends perl-http-tiny:

depends perl-io-all:

depends perl-json:

depends perl-libwww-perl:

depends perl-lockfile-simple:

depends perl-log-log4perl:

depends perl-lwp-simple:

depends perl-math-cdf:

depends perl-mce-shared:

depends perl-net-http:

>=6.18

depends perl-net-ssleay:

depends perl-number-format:

depends perl-object-insideout:

depends perl-parallel-forkmanager:

depends perl-posix:

depends perl-postscript-simple:

depends perl-readonly:

depends perl-statistics-distributions:

depends perl-xml-parser:

depends perl-yaml:

depends pygraphviz:

depends python:

depends pyyaml:

depends r-base:

4.2.3.*

depends r-data.table:

depends r-dendextend:

depends r-dplyr:

depends r-dynamictreecut:

depends r-egg:

depends r-flux:

depends r-ggplot2:

depends r-gplots:

depends r-gridextra:

depends r-jpeg:

depends r-png:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-rjsonio:

depends r-zoo:

depends scipy:

depends seqlogo:

depends snakemake:

>=7.0

depends weblogo:

depends zlib:

>=1.3.1,<2.0a0

requirements:

additional platforms:

linux-aarch64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install rsat-core

and update with::

   mamba update rsat-core

To create a new environment, run:

mamba create --name myenvname rsat-core

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/rsat-core:<tag>

(see `rsat-core/tags`_ for valid values for ``<tag>``)

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.

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