recipe ucsc-fatovcf

Extract VCF from a multi-sequence FASTA alignment.

Homepage:

https://hgdownload.cse.ucsc.edu/admin/exe

Documentation:

https://github.com/ucscGenomeBrowser/kent/blob/master/v482_base/README

Developer docs:

https://github.com/ucscGenomeBrowser/kent

License:

Varies; see https://genome.ucsc.edu/license

Recipe:

/ucsc-fatovcf/meta.yaml

Links:

biotools: UCSC_Genome_Browser_Utilities, doi: 10.1093/bib/bbs038

package ucsc-fatovcf

(downloads) docker_ucsc-fatovcf

versions:

482-1,  482-0,  473-1,  473-0,  448-1,  448-0,  426-0,  407-0

depends bzip2:

>=1.0.8,<2.0a0

depends libgcc:

>=13

depends liblzma:

>=5.8.1,<6.0a0

depends libopenssl-static:

depends libpng:

>=1.6.49,<1.7.0a0

depends libuuid:

>=2.38.1,<3.0a0

depends libzlib:

>=1.3.1,<2.0a0

depends mysql-connector-c:

>=6.1.11,<6.1.12.0a0

requirements:

additional platforms:
linux-aarch64,  osx-arm64

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 ucsc-fatovcf

and update with::

   mamba update ucsc-fatovcf

To create a new environment, run:

mamba create --name myenvname ucsc-fatovcf

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/ucsc-fatovcf:<tag>

(see `ucsc-fatovcf/tags`_ for valid values for ``<tag>``)

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Link to this page

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