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‎_sources/recipes/alpaqa-bio/README.rst.txt‎

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:orphan: .. only available via index, not via toctree
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.. title:: Package Recipe 'alpaqa-bio'
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.. highlight: bash
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alpaqa-bio
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==========
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.. conda:recipe:: alpaqa-bio
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:replaces_section_title:
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:noindex:
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a quality control tool for bacterial ONT\-only assemblies
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:homepage: https://pypi.org/project/alpaqa-bio/
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:license: GPL-3.0-only
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:recipe: /`alpaqa-bio <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/alpaqa-bio>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/alpaqa-bio/meta.yaml>`_
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.. conda:package:: alpaqa-bio
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|downloads_alpaqa-bio| |docker_alpaqa-bio|
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:versions:
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``0.1.4-0``
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:depends on python: ``>=3.9``
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:depends on scipy: ``>=1.10.0``
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:additional platforms:
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Installation
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------------
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You need a conda-compatible package manager
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(currently either `pixi <https://pixi.sh>`__, `conda <https://docs.conda.io/projects/conda>`__, or `micromamba <https://mamba.readthedocs.io>`__)
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and the Bioconda channel already activated (see :ref:`bioconda_setup`).
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Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
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Pixi
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""""
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With pixi_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`),
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to install globally, run::
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pixi global install alpaqa-bio
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to add into an existing workspace instead, run::
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pixi add alpaqa-bio
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In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace::
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pixi workspace channel add conda-forge
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pixi workspace channel add bioconda
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Conda
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"""""
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With conda_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`), to install into an existing and activated environment, run::
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conda install alpaqa-bio
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Alternatively, to install into a new environment, run::
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conda create -n envname alpaqa-bio
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with ``envname`` being the name of the desired environment.
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Container
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"""""""""
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Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime.
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For e.g. docker, run::
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docker pull quay.io/biocontainers/alpaqa-bio:<tag>
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(see `alpaqa-bio/tags`_ for valid values for ``<tag>``).
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Integrated deployment
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"""""""""""""""""""""
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Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment.
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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.
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Check the documentation of your workflow management system to find out about the integration.
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.. _conda: https://conda.io
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.. _pixi: https://pixi.sh
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.. |downloads_alpaqa-bio| image:: https://img.shields.io/conda/dn/bioconda/alpaqa-bio.svg?style=flat
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:target: https://anaconda.org/bioconda/alpaqa-bio
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:alt: (downloads)
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.. |docker_alpaqa-bio| image:: https://quay.io/repository/biocontainers/alpaqa-bio/status
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:target: https://quay.io/repository/biocontainers/alpaqa-bio
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.. _`alpaqa-bio/tags`: https://quay.io/repository/biocontainers/alpaqa-bio?tab=tags
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.. raw:: html
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<script>
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var package = "alpaqa-bio";
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var versions = ["0.1.4"];
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</script>
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Download stats
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-----------------
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.. raw:: html
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:file: ../../templates/package_dashboard.html
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Link to this page
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-----------------
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Render an |install-with-bioconda| badge with the following MarkDown::
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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/alpaqa-bio/README.html)
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.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
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:target: http://bioconda.github.io/recipes/alpaqa-bio/README.html

‎_sources/recipes/atol-genome-launcher/README.rst.txt‎

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.. raw:: html
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<details><summary><span class="truncated-version-list"><code>0.8.0-0</code>,  <code>0.7.5-0</code>,  <code>0.7.4-0</code>,  <code>0.7.2-0</code>,  <code>0.7.1-0</code>,  <code>0.7.0-0</code>,  <code>0.6.0-0</code>,  <code>0.5.5-0</code>,  <code>0.5.4-0</code>,  </span></summary>
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<details><summary><span class="truncated-version-list"><code>0.8.2-0</code>,  <code>0.8.1-0</code>,  <code>0.8.0-0</code>,  <code>0.7.5-0</code>,  <code>0.7.4-0</code>,  <code>0.7.2-0</code>,  <code>0.7.1-0</code>,  <code>0.7.0-0</code>,  <code>0.6.0-0</code>,  </span></summary>
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``0.8.0-0``,  ``0.7.5-0``,  ``0.7.4-0``,  ``0.7.2-0``,  ``0.7.1-0``,  ``0.7.0-0``,  ``0.6.0-0``,  ``0.5.5-0``,  ``0.5.4-0``,  ``0.5.3-0``,  ``0.5.2-0``,  ``0.5.1-0``,  ``0.5.0-0``,  ``0.4.1-0``,  ``0.4.0-0``,  ``0.3.1-0``,  ``0.2.1-0``,  ``0.2.0-0``,  ``0.1.5-0``
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``0.8.2-0``,  ``0.8.1-0``,  ``0.8.0-0``,  ``0.7.5-0``,  ``0.7.4-0``,  ``0.7.2-0``,  ``0.7.1-0``,  ``0.7.0-0``,  ``0.6.0-0``,  ``0.5.5-0``,  ``0.5.4-0``,  ``0.5.3-0``,  ``0.5.2-0``,  ``0.5.1-0``,  ``0.5.0-0``,  ``0.4.1-0``,  ``0.4.0-0``,  ``0.3.1-0``,  ``0.2.1-0``,  ``0.2.0-0``,  ``0.1.5-0``
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:depends on ca-certificates:
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:depends on git:
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:depends on pandas: ``>=2.3.3,<3``
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:depends on pigz:
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:depends on pydantic: ``>=2.12.5``
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<script>
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var package = "atol-genome-launcher";
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var versions = ["0.8.0","0.7.5","0.7.4","0.7.2","0.7.1"];
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var versions = ["0.8.2","0.8.1","0.8.0","0.7.5","0.7.4"];
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</script>
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‎_sources/recipes/bigsdb-downloader/README.rst.txt‎

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:orphan: .. only available via index, not via toctree
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.. title:: Package Recipe 'bigsdb-downloader'
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.. highlight: bash
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bigsdb-downloader
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=================
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.. conda:recipe:: bigsdb-downloader
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:replaces_section_title:
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:noindex:
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BIGSdb Downloader
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:homepage: https://github.com/kjolley/BIGSdb_downloader
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:license: GPL-3.0-or-later
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:recipe: /`bigsdb-downloader <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bigsdb-downloader>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bigsdb-downloader/meta.yaml>`_
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.. conda:package:: bigsdb-downloader
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|downloads_bigsdb-downloader| |docker_bigsdb-downloader|
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:versions:
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``1.0.5-0``
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:depends on python: ``>=3.9``
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:depends on rauth: ``>=0.7.3``
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:additional platforms:
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Installation
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------------
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You need a conda-compatible package manager
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(currently either `pixi <https://pixi.sh>`__, `conda <https://docs.conda.io/projects/conda>`__, or `micromamba <https://mamba.readthedocs.io>`__)
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and the Bioconda channel already activated (see :ref:`bioconda_setup`).
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Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
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Pixi
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""""
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With pixi_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`),
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to install globally, run::
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pixi global install bigsdb-downloader
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to add into an existing workspace instead, run::
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pixi add bigsdb-downloader
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In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace::
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pixi workspace channel add conda-forge
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pixi workspace channel add bioconda
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Conda
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"""""
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With conda_ installed and the Bioconda channel set up (see :ref:`bioconda_setup`), to install into an existing and activated environment, run::
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conda install bigsdb-downloader
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Alternatively, to install into a new environment, run::
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conda create -n envname bigsdb-downloader
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with ``envname`` being the name of the desired environment.
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Container
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"""""""""
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Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime.
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For e.g. docker, run::
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docker pull quay.io/biocontainers/bigsdb-downloader:<tag>
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(see `bigsdb-downloader/tags`_ for valid values for ``<tag>``).
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Integrated deployment
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"""""""""""""""""""""
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Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment.
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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.
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Check the documentation of your workflow management system to find out about the integration.
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.. _conda: https://conda.io
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.. _pixi: https://pixi.sh
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.. |downloads_bigsdb-downloader| image:: https://img.shields.io/conda/dn/bioconda/bigsdb-downloader.svg?style=flat
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:target: https://anaconda.org/bioconda/bigsdb-downloader
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:alt: (downloads)
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.. |docker_bigsdb-downloader| image:: https://quay.io/repository/biocontainers/bigsdb-downloader/status
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:target: https://quay.io/repository/biocontainers/bigsdb-downloader
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.. _`bigsdb-downloader/tags`: https://quay.io/repository/biocontainers/bigsdb-downloader?tab=tags
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.. raw:: html
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<script>
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var package = "bigsdb-downloader";
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var versions = ["1.0.5"];
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</script>
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Download stats
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-----------------
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.. raw:: html
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:file: ../../templates/package_dashboard.html
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Link to this page
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-----------------
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Render an |install-with-bioconda| badge with the following MarkDown::
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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bigsdb-downloader/README.html)
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.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
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:target: http://bioconda.github.io/recipes/bigsdb-downloader/README.html

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