recipe usher

Ultrafast Sample Placement on Existing Trees (UShER)

Homepage:

https://github.com/yatisht/usher

Documentation:

https://usher-wiki.readthedocs.io/en/latest/

License:

MIT / MIT

Recipe:

/usher/meta.yaml

Links:

doi: 10.1038/s41588-021-00862-7

package usher

versions:

0.6.3-1,  0.6.3-0,  0.6.2-1,  0.6.2-0,  0.6.1-1,  0.6.1-0,  0.6.0-0,  0.5.6-2,  0.5.6-1, 

0.6.3-1,  0.6.3-0,  0.6.2-1,  0.6.2-0,  0.6.1-1,  0.6.1-0,  0.6.0-0,  0.5.6-2,  0.5.6-1,  0.5.6-0,  0.5.5-0,  0.5.4-1,  0.5.4-0,  0.5.3-0,  0.5.2-2,  0.5.2-1,  0.5.2-0,  0.5.1-0,  0.5.0-1,  0.5.0-0,  0.4.8-4,  0.4.8-0,  0.4.7-0,  0.4.6-0,  0.4.4-0,  0.4.3-0,  0.4.2-0,  0.4.1-0,  0.4.0-1,  0.4.0-0,  0.3.5-0,  0.3.4-0,  0.3.2-0,  0.3.1-1,  0.3.1-0,  0.2.1-0,  0.2.0-1,  0.2.0-0,  0.1.3-0

depends boost-cpp:

>=1.78.0,<1.78.1.0a0

depends isa-l:

depends libgcc-ng:

>=12

depends libprotobuf:

>=3.21.12,<3.22.0a0

depends libstdcxx-ng:

>=12

depends mafft:

depends openmpi:

4.1.2.*

depends openmpi:

>=4.1.2,<5.0a0

depends openssh:

depends ucsc-fatovcf:

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 usher

and update with::

   mamba update usher

To create a new environment, run:

mamba create --name myenvname usher

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/usher:<tag>

(see `usher/tags`_ for valid values for ``<tag>``)

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