recipe bacpage

An easy-to-use pipeline for the assembly and analysis of bacterial genomes

Homepage:

https://github.com/CholGen/bacpage

Documentation:

https://cholgen.github.io/sequencing-resources/bacpage-command.html

License:

GPL3 / GPL-3.0-or-later

Recipe:

/bacpage/meta.yaml

package bacpage

versions:

2024.03.08-0,  2023.11.10.1-0

depends abricate:

depends bc:

depends bcftools:

1.17.*

depends bedtools:

depends biopython:

depends bwa:

depends emboss:

depends fastp:

depends fastqc:

depends flash:

depends iqtree:

depends lighter:

depends multiqc:

depends pandas:

depends prokka:

depends python:

>=3.9,<3.12

depends qualimap:

depends quast:

depends samtools:

1.17.*

depends snakemake-minimal:

depends snp-sites:

depends unicycler:

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 bacpage

and update with::

   mamba update bacpage

To create a new environment, run:

mamba create --name myenvname bacpage

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/bacpage:<tag>

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

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