recipe ucsc-lavtoaxt

Convert blastz lav file to an axt file (which includes sequence)

Homepage:

https://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-lavtoaxt/meta.yaml

Links:

biotools: UCSC_Genome_Browser_Utilities, doi: 10.1093/bib/bbs038

package ucsc-lavtoaxt

versions:

469-0,  377-3,  377-2,  377-1,  377-0,  366-0,  357-2,  357-1,  357-0

depends libgcc-ng:

>=12

depends libopenssl-static:

depends libpng:

>=1.6.43,<1.7.0a0

depends libuuid:

>=2.38.1,<3.0a0

depends libzlib:

>=1.2.13,<2.0a0

depends mysql-connector-c:

>=6.1.11,<6.1.12.0a0

depends zlib:

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 ucsc-lavtoaxt

and update with::

   mamba update ucsc-lavtoaxt

To create a new environment, run:

mamba create --name myenvname ucsc-lavtoaxt

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-lavtoaxt:<tag>

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

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