recipe bioconvert

Convert between bioinformatics formats

Homepage:

https://pypi.org/project/bioconvert/

Documentation:

https://bioconvert.readthedocs.io/en/dev/

Developer docs:

https://github.com/bioconvert/bioconvert

License:

GPL-3.0

Recipe:

/bioconvert/meta.yaml

package bioconvert

versions:

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, 

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 bamtools:

depends bcftools:

depends bedops:

depends bedtools:

depends biopython:

>=1.70

depends biosniff:

depends colorlog:

depends deeptools:

depends dsrc:

depends easydev:

depends gffread:

depends go:

1.10.*

depends graphviz:

depends jinja2:

<3.1

depends mappy:

depends matplotlib-base:

depends mawk:

depends mosdepth:

depends networkx:

depends numpydoc:

depends openpyxl:

<=3.0.10

depends pandas:

depends pbzip2:

depends picard-slim:

depends pigz:

depends plink:

depends psutil:

depends py2bit:

depends pybigwig:

depends pyexcel:

depends pyexcel-ods3:

depends pyexcel-xls:

depends pyexcel-xlsx:

depends pysam:

depends python:

>=3.8

depends pyyaml:

depends sambamba:

depends samtools:

>=1.17

depends sed:

depends seqkit:

depends seqtk:

depends squizz:

depends sra-tools:

depends statsmodels:

depends tqdm:

depends ucsc-bedgraphtobigwig:

depends ucsc-bigwigtobedgraph:

depends ucsc-fatotwobit:

depends ucsc-twobittofa:

depends ucsc-wigtobigwig:

depends wiggletools:

1.2.*

depends xlrd:

>2.0

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 bioconvert

and update with::

   mamba update bioconvert

To create a new environment, run:

mamba create --name myenvname bioconvert

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/bioconvert:<tag>

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

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