recipe bioconductor-contibait

Improves Early Build Genome Assemblies using Strand-Seq Data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/contiBAIT.html

License:

BSD_2_clause + file LICENSE

Recipe:

/bioconductor-contibait/meta.yaml

Links:

biotools: contibait, doi: 10.1093/bioinformatics/btx281

Using strand inheritance data from multiple single cells from the organism whose genome is to be assembled, contiBAIT can cluster unbridged contigs together into putative chromosomes, and order the contigs within those chromosomes.

package bioconductor-contibait

(downloads) docker_bioconductor-contibait

versions:
1.30.0-11.30.0-01.28.0-01.26.0-11.26.0-01.22.0-21.22.0-11.22.0-01.20.0-0

1.30.0-11.30.0-01.28.0-01.26.0-11.26.0-01.22.0-21.22.0-11.22.0-01.20.0-01.18.0-11.18.0-01.15.0-01.14.0-01.12.0-11.10.0-01.8.0-01.6.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocgenerics:

>=0.48.1,<0.49.0a0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0a0

depends bioconductor-dnacopy:

>=1.76.0,<1.77.0

depends bioconductor-dnacopy:

>=1.76.0,<1.77.0a0

depends bioconductor-exomecopy:

>=1.48.0,<1.49.0

depends bioconductor-exomecopy:

>=1.48.0,<1.49.0a0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0a0

depends bioconductor-genomicfiles:

>=1.38.0,<1.39.0

depends bioconductor-genomicfiles:

>=1.38.0,<1.39.0a0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.1,<1.55.0a0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0a0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0a0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0a0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-s4vectors:

>=0.40.2,<0.41.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-bh:

>=1.51.0.3

depends r-clue:

depends r-cluster:

depends r-colorspace:

depends r-data.table:

depends r-diagram:

depends r-ggplot2:

depends r-gplots:

depends r-gtools:

depends r-rcpp:

depends r-reshape2:

depends r-tsp:

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 bioconductor-contibait

and update with::

   mamba update bioconductor-contibait

To create a new environment, run:

mamba create --name myenvname bioconductor-contibait

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/bioconductor-contibait:<tag>

(see `bioconductor-contibait/tags`_ for valid values for ``<tag>``)

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