Package Recipe 'ymp'

recipe ymp

Create entire NGS pipelines with one command

Homepage:: https://ymp.readthedocs.io
Developer docs:: https://github.com/epruesse/ymp
License:: GPL3 / GNU General Public v3 or later (GPLv3+)
Recipe:: /ymp/meta.yaml

YMP allows composing complex NGS data analysis workflows from conceptual building blocks ("stages") using a single command line statement. Pre-tested conda environments are installed on-the fly, reference databases downloaded as needed and requested workflows executed using Snakemake.

With YMP, developing new pipelines or testing alternative approaches using differnt tools or optimizing parameters becomes easy. Results from previous results are reused where possible. The collection of stages included with YMP is can be extended with project specific YMP stage definitions or simple Snakefiles.

package ymp¶

Versions:

0.3.2-0, 0.3.1-0, 0.2.1-0, 0.1.0-0

Depends:

on aiohttp
on click >8
on click-completion
on coloredlogs
on conda
on drmaa
on mamba
on networkx >=2
on openpyxl
on pandas >=0.20
on python >=3.10
on ruamel.yaml >0.15
on snakemake >=7.32.1,<8.0a0
on tqdm >=4.21.0
on xdg
on xlrd

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 ymp

to add into an existing workspace instead, run:

pixi add ymp

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 ymp

Alternatively, to install into a new environment, run:

conda create -n envname ymp

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/ymp:<tag>

(see ymp/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/ymp/README.html)