recipe assembly_uploader

Python scripts to upload primary metagenome and metatranscriptome assemblies to ENA on a per-study basis. The scripts generate xmls to register a new study and create manifests necessary for submission with webin-cli.

Homepage:

https://github.com/EBI-Metagenomics/assembly_uploader

Documentation:

https://github.com/EBI-Metagenomics/assembly_uploader/blob/main/README.md

License:

APACHE / Apache-2.0

Recipe:

/assembly_uploader/meta.yaml

package assembly_uploader

(downloads) docker_assembly_uploader

versions:

1.3.2-0

depends python:

>=3.8

depends requests:

2.32.3

requirements:

additional platforms:

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 assembly_uploader

and update with::

   mamba update assembly_uploader

To create a new environment, run:

mamba create --name myenvname assembly_uploader

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/assembly_uploader:<tag>

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

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Link to this page

Render an install-with-bioconda 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/assembly_uploader/README.html)