Package Recipe 'onebam'

recipe onebam

ONEcode replacement for SAM/BAM in large-scale eDNA mapping and taxonomic analysis

Homepage:: https://github.com/richarddurbin/onebam
License:: MIT / MIT
Recipe:: /onebam/meta.yaml

onebam converts read-sorted SAM/BAM/CRAM files into a compact ONEcode .1read format, storing reads with sequences, quality scores, best-match damage information, and taxonomy hit data. It supports merging, LCA (Lowest Common Ancestor) assignment, taxonomic reporting, and read extraction, making it suitable for eDNA workflows mapping against very large reference databases such as all of NCBI.

package onebam¶

Versions:

0-0

Depends:

on bzip2 >=1.0.8,<2.0a0
on htslib >=1.23.1,<1.24.0a0
on libcurl >=8.19.0,<9.0a0
on libgcc >=14
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.2,<2.0a0
on xz
on zlib
on zstd >=1.5.7,<1.6.0a0

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 onebam

to add into an existing workspace instead, run:

pixi add onebam

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 onebam

Alternatively, to install into a new environment, run:

conda create -n envname onebam

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/onebam:<tag>

(see onebam/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/onebam/README.html)