recipe rsat-core

Detection of regulatory signals in non-coding sequences.

Homepage:

http://rsat.eu/

License:

AGPL-3

Recipe:

/rsat-core/meta.yaml

Links:

biotools: rsat, doi: 10.1093/nar/gky317

package rsat-core

versions:

2020.02.29-1,  2020.02.29-0,  2020.02.28-0,  2020.01.04-0

depends bedtools:

depends bioconductor-ctc:

depends bioconductor-qvalue:

depends blast:

depends d3:

depends ghostscript:

depends gnuplot:

depends httplib2:

depends libcxx:

>=9.0.1

depends libgfortran:

>=4.0.0,<5.0.0.a0

depends matplotlib:

depends numpy:

depends perl:

>=5.26.2,<5.26.3.0a0

depends perl-algorithm-cluster:

depends perl-bio-das:

depends perl-bioperl:

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-digest-md5-file:

depends perl-email-simple:

depends perl-ensembl-api:

depends perl-ensembl-genomes:

depends perl-file-spec:

depends perl-gd:

depends perl-http-tiny:

depends perl-io-all:

depends perl-json:

depends perl-lockfile-simple:

depends perl-log-log4perl:

depends perl-lwp-simple:

depends perl-math-cdf:

depends perl-mce-shared:

depends perl-number-format:

depends perl-object-insideout:

depends perl-ole-storage_lite:

depends perl-parallel-forkmanager:

depends perl-posix:

depends perl-readonly:

depends perl-rest-client:

depends perl-soap-lite:

depends perl-spreadsheet-writeexcel:

depends perl-statistics-distributions:

depends perl-util-properties:

depends perl-xml-dom:

depends perl-xml-libxml:

depends perl-xml-parser:

depends perl-yaml:

depends pygraphviz:

depends python:

>=3.6,<3.7.0a0

depends python_abi:

3.6.* *_cp36m

depends pyyaml:

depends r-amap:

depends r-base:

>=4.0,<4.1.0a0

depends r-data.table:

depends r-dendextend:

depends r-devtools:

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:

depends vmatch:

depends weblogo:

requirements:

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>``)

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