recipe ucsc-bedjointaboffset

given a bed file and tab file where each have a column with matching values: first get the value of column0, the offset and line length from inTabFile. Then go over the bed file, use the name field and append its offset and length to the bed file as two separate fields. Write the new bed file to outBed.

Homepage:

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

Documentation:

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

Developer docs:

https://github.com/ucscGenomeBrowser/kent

License:

varies; see http://genome.ucsc.edu/license

Recipe:

/ucsc-bedjointaboffset/meta.yaml

Links:

biotools: UCSC_Genome_Browser_Utilities, doi: 10.1093/bib/bbs038

package ucsc-bedjointaboffset

versions:

377-2,  377-1,  377-0,  366-0

depends libpng:

depends libuuid:

depends mysql-connector-c:

depends openssl:

>=1.1.0,<=1.1.1

depends python:

depends zlib:

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 ucsc-bedjointaboffset

and update with::

   mamba update ucsc-bedjointaboffset

To create a new environment, run:

mamba create --name myenvname ucsc-bedjointaboffset

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-bedjointaboffset:<tag>

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

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