Package Recipe 'aquamis'

recipe aquamis

AQUAMIS is a snakemake pipeline for routine assembly and quality assessment of microbial isolate sequencing experiments.

Homepage:: https://gitlab.com/bfr_bioinformatics/AQUAMIS
License:: BSD-3
Recipe:: /aquamis/meta.yaml

package aquamis¶

Versions:

1.4.0-0, 1.3.7-0, 1.3.6-0, 1.3.5-0, 1.3.4-0, 1.3.3-0, 1.3.0-0

Depends:

on bbmap >=39
on biopython >=1.79
on blast >=2.14
on bracken >=2.8
on bwa >=0.7.17
on cerberus >=1.3.4
on circos >=0.69.9
on confindr 0.7.4.*
on entrez-direct >=16.2
on fastp >=0.23.2
on genson >=1.2.2
on jsonschema >=4.17
on kma >=1.2
on kmc >=3.2.1
on kraken2 >=2.1.3
on mash >=2.3
on minimap2 >=2.26
on mlst >=2.23
on numpy >=1.21
on pandas >=1.3.5
on pandoc >=2.19
on perl-bio-tools-run-alignment-tcoffee 1.7.4 pl5321hdfd78af_4
on pilon >=1.24
on python 3.7.*
on pyyaml >=6
on quast >=5.2.0
on r-base 4.0.*
on r-dt >=0.25
on r-knitr >=1.40
on r-rmarkdown >=2.16
on r-rrapply >=1.2.5
on r-tidyverse >=1.3.2
on r-urltools >=1.7.3
on samtools >=1.12
on seqtk >=1.4
on shovill >=1.1.0
on snakemake-minimal 7.*
on spades >=3.15
on taxonkit >=0.15
on trimmomatic >=0.39
on tzdata

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 aquamis

to add into an existing workspace instead, run:

pixi add aquamis

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 aquamis

Alternatively, to install into a new environment, run:

conda create -n envname aquamis

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/aquamis:<tag>

(see aquamis/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/aquamis/README.html)