recipe b2b-utils

Genomics tools from BASE2BIO

Homepage:

https://github.com/jvolkening/b2b-utils

License:

GPL3 / GPL-3.0-or-later

Recipe:

/b2b-utils/meta.yaml

This package contains a set of programs and utilities for working with genomic data. Please see the in-program documentation (`--help`) of each individual tool for usage and details. Please note that some tools in this suite utilize dependencies that are not explicity stated in the Conda package. This keeps the install footprint smaller since all users will not use all utilities, but if you receive error messages about missing programs you will need to install those as well. All possible dependencies should be available as Conda packages.

package b2b-utils

(downloads) docker_b2b-utils

versions:

0.019-0,  0.018-0,  0.017-0

depends mafft:

>=7.520,<8.0a0

depends minimap2:

>=2.26,<3.0a0

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

depends perl-bioperl:

depends perl-biox-seq:

>=0.008006

depends perl-dbi:

depends perl-list-moreutils:

depends perl-module-build:

0.4234.*

depends perl-perlio-gzip:

depends samtools:

>=1.18,<2.0a0

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 b2b-utils

and update with::

   mamba update b2b-utils

To create a new environment, run:

mamba create --name myenvname b2b-utils

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/b2b-utils:<tag>

(see `b2b-utils/tags`_ for valid values for ``<tag>``)

Notes

  • Can't be noarch or mulled testing fails because perl-dbi dependency is

not pulled in

  • Extra packages (bwa, samtools, etc) are included in host deps so that

the full testing suite will be run during building, but they are not added to run-time deps since not all users may need the corresponding utilities. This decision may be revisited in the future.

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