Package Recipe 'abromics_galaxy_json_extractor'

recipe abromics_galaxy_json_extractor

Tool to convert Galaxy AMR output to abromics project

Homepage:: ifb-elixirfr/abromics
Documentation:: ifb-elixirfr/abromics/abromics-galaxy-json-extractor/-/blob/main/docs/_build/html/index.html
Developer docs:: ifb-elixirfr/abromics/abromics-galaxy-json-extractor
License:: GPL / GPLv3
Recipe:: /abromics_galaxy_json_extractor/meta.yaml

package abromics_galaxy_json_extractor#

Versions:

0.8.3.6-0, 0.8.3.5-0, 0.8.3.4-0, 0.8.3-0, 0.8.2.1-0, 0.8.2-0, 0.8.1-0, 0.8-0, 0.7-0,

0.8.3.6-0, 0.8.3.5-0, 0.8.3.4-0, 0.8.3-0, 0.8.2.1-0, 0.8.2-0, 0.8.1-0, 0.8-0, 0.7-0, 0.6-0, 0.5-0, 0.4-0, 0.2-0, 0.1-1, 0.1-0

Depends:

on _libgcc_mutex
on _openmp_mutex
on biopython
on bzip2
on ca-certificates
on ld_impl_linux-64
on libblas
on libcblas
on libffi
on libgcc-ng
on libgfortran-ng
on libgfortran5
on libgomp
on liblapack
on libnsl
on libopenblas
on libsqlite
on libstdcxx-ng
on libzlib
on ncurses
on numpy
on openssl
on pandas
on pip
on python
on python-dateutil
on python-tzdata
on python_abi
on pytz
on readline
on setuptools
on six
on tk
on tzdata
on wheel
on xz

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 abromics_galaxy_json_extractor

to add into an existing workspace instead, run:

pixi add abromics_galaxy_json_extractor

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 abromics_galaxy_json_extractor

Alternatively, to install into a new environment, run:

conda create -n envname abromics_galaxy_json_extractor

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/abromics_galaxy_json_extractor:<tag>

(see abromics_galaxy_json_extractor/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

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

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/abromics_galaxy_json_extractor/README.html)