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:

0.2.1-0,  0.1.0-0

depends aiohttp:

depends click:

depends click-completion:

depends coloredlogs:

depends conda:

depends drmaa:

depends networkx:

>=2

depends pandas:

>=0.20

depends python:

>=3.6

depends ruamel.yaml:

>0.15

depends snakemake:

>=5.20.1,<5.21.0a0

depends tqdm:

>=4.21.0

depends xdg:

depends xlrd:

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 ymp

and update with::

   mamba update ymp

To create a new environment, run:

mamba create --name myenvname ymp

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/ymp:<tag>

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

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