Package Recipe 'b2b-utils'

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¶

Versions:

0.020-0, 0.019-0, 0.018-0, 0.017-0

Depends:

on bwa >=0.7.18,<0.8.0a0
on mafft >=7.526,<8.0a0
on medaka >=2.0.1,<3.0a0
on miniasm >=0.3,<0.4.0a0
on minimap2 >=2.28,<3.0a0
on perl >=5.32.1,<5.33.0a0 *_perl5
on perl-bioperl
on perl-biox-seq >=0.008006
on perl-biox-seq >=0.8009,<1.0a0
on perl-dbi
on perl-list-moreutils
on perl-module-build 0.4234.*
on perl-perlio-gzip >=0.20,<0.21.0a0
on samtools >=1.21,<2.0a0

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install b2b-utils

to add into an existing workspace instead, run:

pixi add b2b-utils

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install b2b-utils

Alternatively, to install into a new environment, run:

conda create -n envname b2b-utils

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/b2b-utils:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/b2b-utils/README.html)