Package Recipe 'bioconvert'

recipe bioconvert

Convert between bioinformatics formats.

Homepage:: https://github.com/bioconvert/bioconvert
Documentation:: https://bioconvert.readthedocs.io/en/dev
License:: GPL3 / GPL-3.0-or-later
Recipe:: /bioconvert/meta.yaml

package bioconvert¶

Versions:

1.2.0-0, 1.1.1-3, 1.1.1-2, 1.1.1-1, 1.1.1-0, 1.1.0-0, 1.0.0.post0-0, 0.6.3-0, 0.6.2-0,

1.2.0-0, 1.1.1-3, 1.1.1-2, 1.1.1-1, 1.1.1-0, 1.1.0-0, 1.0.0.post0-0, 0.6.3-0, 0.6.2-0, 0.6.1-0, 0.6.0-0, 0.5.2-0, 0.4.3-0, 0.4.2-0, 0.4.1-0, 0.4.0-0, 0.3.0-1, 0.2.0-2, 0.2.0-1, 0.0.10-1, 0.0.10-0

Depends:

on bamtools
on bcftools
on bedops
on bedtools
on biopython >=1.70
on biosniff
on colorlog
on deeptools
on dsrc
on easydev
on gffread
on go 1.24.*
on goalign
on gotree
on graphviz
on htslib
on jinja2 <3.1
on mappy
on matplotlib-base
on mawk
on mosdepth
on networkx
on numpydoc
on openpyxl <=3.0.10
on pandas
on pbzip2
on picard-slim
on pigz
on plink
on psutil
on py2bit
on pybigwig
on pyexcel
on pyexcel-ods3
on pyexcel-xls
on pyexcel-xlsx
on pysam
on python >=3.8
on pyyaml
on rich-click
on sambamba
on samtools
on sed
on seqkit
on seqtk
on squizz
on sra-tools
on statsmodels
on tqdm
on ucsc-bedgraphtobigwig
on ucsc-bigwigtobedgraph
on ucsc-fatotwobit
on ucsc-twobittofa
on ucsc-wigtobigwig
on wiggletools
on xlrd >2.0

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 bioconvert

to add into an existing workspace instead, run:

pixi add bioconvert

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 bioconvert

Alternatively, to install into a new environment, run:

conda create -n envname bioconvert

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/bioconvert:<tag>

(see bioconvert/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.

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/bioconvert/README.html)