Package Recipe 'pathogen-profiler'

recipe pathogen-profiler

Library giving access to classes and functions to create a profiling tool to look for mutations from NGS data.

Homepage:: https://github.com/jodyphelan/pathogen-profiler
License:: GPL3
Recipe:: /pathogen-profiler/meta.yaml

package pathogen-profiler¶

Versions:

5.1.0-0, 5.0.3-0, 5.0.2-0, 5.0.1-0, 5.0.0-0, 4.8.0-0, 4.7.0-0, 4.6.0-0, 4.5.1-0,

5.1.0-0, 5.0.3-0, 5.0.2-0, 5.0.1-0, 5.0.0-0, 4.8.0-0, 4.7.0-0, 4.6.0-0, 4.5.1-0, 4.5.0-1, 4.5.0-0, 4.4.0-0, 4.3.0-0, 4.2.0-1, 4.2.0-0, 4.1.0-0, 4.0.0-0, 3.1.0-0, 3.0.0-0, 2.0.4-1, 2.0.4-0, 2.0.3-0, 2.0.2-1, 2.0.2-0, 2.0.1-0, 2.0.0-1, 2.0.0-0, 1.7.3-1, 1.7.3-0, 1.7.2-0, 1.7.1-1, 1.7.1-0, 1.7-0, 1.6.1-0, 1.6-0, 1.5-0, 1.3-0, 1.2-0, 1.1-2, 1.1-1, 1.1-0, 1.0-0, 0.1-3, 0.1-2, 0.1-1, 0.1-0

Depends:

on bcftools >=1.12
on bedtools
on bwa
on delly 1.3.3.*
on dsk >=2.2
on filelock
on freebayes 1.3.6.*
on gatk4
on git
on itol-config
on joblib >=1.3.0
on kmc >=3.2.1
on lofreq >=2.1.5
on minimap2 >=2.28
on openjdk >=11.0.8
on pandas
on parallel
on pilon >=1.24
on pydantic >=2.6
on pysam
on python >=3.10
on requests
on rich-argparse
on samclip
on samtools >=1.12
on seqkit
on snpeff 5.2.*
on sourmash
on sylph
on tomli
on tqdm
on trimmomatic

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 pathogen-profiler

to add into an existing workspace instead, run:

pixi add pathogen-profiler

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 pathogen-profiler

Alternatively, to install into a new environment, run:

conda create -n envname pathogen-profiler

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/pathogen-profiler:<tag>

(see pathogen-profiler/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/pathogen-profiler/README.html)