- recipe bacpage
An easy-to-use pipeline for the assembly and analysis of bacterial genomes.
- Homepage:
- Documentation:
https://cholgen.github.io/sequencing-resources/bacpage-command.html
- License:
GPL3 / GPL-3.0-or-later
- Recipe:
- package bacpage¶
- Versions:
2025.08.21-0,2024.03.08-0,2023.11.10.1-0- Depends:
on abricate
on bc
on bcftools
on bedtools
on biopython
on bwa
on emboss
on fastp
on fastqc
on flash
on iqtree
on lighter
on multiqc
on pandas
on prokka
on python
>=3.9,<3.12on qualimap
on quast
on samtools
on snakemake-minimal
<8on snp-sites
on unicycler
- 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 bacpage
to add into an existing workspace instead, run:
pixi add bacpage
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 bacpage
Alternatively, to install into a new environment, run:
conda create -n envname bacpage
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/bacpage:<tag>
(see bacpage/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:
[](http://bioconda.github.io/recipes/bacpage/README.html)
