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‎_sources/recipes/atlas-fastq-provider/README.rst.txt‎

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``0.4.8-0``,  ``0.4.7-0``,  ``0.4.6-0``,  ``0.4.5-0``,  ``0.4.4-0``,  ``0.4.3-0``,  ``0.4.2-0``,  ``0.4.1-0``
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``0.4.9-0``,  ``0.4.8-0``,  ``0.4.7-0``,  ``0.4.6-0``,  ``0.4.5-0``,  ``0.4.4-0``,  ``0.4.3-0``,  ``0.4.2-0``,  ``0.4.1-0``
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<script>
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var package = "atlas-fastq-provider";
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var versions = ["0.4.9","0.4.8","0.4.7","0.4.6","0.4.5"];
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‎_sources/recipes/atol-genome-launcher/README.rst.txt‎

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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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<details><summary><span class="truncated-version-list"><code>0.8.3-0</code>,  <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>,  </span></summary>
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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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``0.8.3-0``,  ``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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‎_sources/recipes/bbmap/README.rst.txt‎

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<details><summary><span class="truncated-version-list"><code>39.80-0</code>,  <code>39.79-0</code>,  <code>39.77-0</code>,  <code>39.76-0</code>,  <code>39.52-0</code>,  <code>39.50-0</code>,  <code>39.37-0</code>,  <code>39.33-0</code>,  <code>39.28-0</code>,  </span></summary>
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<details><summary><span class="truncated-version-list"><code>39.81-0</code>,  <code>39.80-0</code>,  <code>39.79-0</code>,  <code>39.77-0</code>,  <code>39.76-0</code>,  <code>39.52-0</code>,  <code>39.50-0</code>,  <code>39.37-0</code>,  <code>39.33-0</code>,  </span></summary>
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``39.80-0``,  ``39.79-0``,  ``39.77-0``,  ``39.76-0``,  ``39.52-0``,  ``39.50-0``,  ``39.37-0``,  ``39.33-0``,  ``39.28-0``,  ``39.26-0``,  ``39.25-0``,  ``39.24-0``,  ``39.19-0``,  ``39.18-0``,  ``39.17-0``,  ``39.15-0``,  ``39.13-1``,  ``39.13-0``,  ``39.11-0``,  ``39.10-0``,  ``39.09-0``,  ``39.08-0``,  ``39.06-1``,  ``39.06-0``,  ``39.01-1``,  ``39.01-0``,  ``39.00-0``,  ``38.99-0``,  ``38.98-1``,  ``38.98-0``,  ``38.97-1``,  ``38.97-0``,  ``38.96-1``,  ``38.96-0``,  ``38.95-1``,  ``38.95-0``,  ``38.93-0``,  ``38.92-0``,  ``38.91-1``,  ``38.91-0``,  ``38.90-3``,  ``38.90-2``,  ``38.90-1``,  ``38.90-0``,  ``38.89-0``,  ``38.88-0``,  ``38.87-0``,  ``38.86-0``,  ``38.84-1``,  ``38.84-0``,  ``38.79-0``,  ``38.76-0``,  ``38.75-0``,  ``38.73-0``,  ``38.72-0``,  ``38.71-0``,  ``38.70-0``,  ``38.69-0``,  ``38.68-0``,  ``38.67-0``,  ``38.65-0``,  ``38.63-0``,  ``38.62-0``,  ``38.61b-0``,  ``38.58-0``,  ``38.57-0``,  ``38.56-0``,  ``38.51-0``,  ``38.49-0``,  ``38.46-0``,  ``38.45-0``,  ``38.44-0``,  ``38.22-1``,  ``38.22-0``,  ``38.20-0``,  ``38.19-0``,  ``38.18-0``,  ``38.16-0``,  ``38.06-2``,  ``38.06-0``,  ``37.99-1``,  ``37.99-0``,  ``37.96-0``,  ``37.95-0``,  ``37.90-0``,  ``37.78-0``,  ``37.77-0``,  ``37.75-0``,  ``37.66-0``,  ``37.62-2``,  ``37.62-1``,  ``37.62-0``,  ``37.52-1``,  ``37.52-0``,  ``37.17-1``,  ``37.17-0``,  ``37.10-1``,  ``37.10-0``,  ``37.02-0``,  ``36.84-0``,  ``36.32-0``,  ``35.85-2``,  ``35.85-1``
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``39.81-0``,  ``39.80-0``,  ``39.79-0``,  ``39.77-0``,  ``39.76-0``,  ``39.52-0``,  ``39.50-0``,  ``39.37-0``,  ``39.33-0``,  ``39.28-0``,  ``39.26-0``,  ``39.25-0``,  ``39.24-0``,  ``39.19-0``,  ``39.18-0``,  ``39.17-0``,  ``39.15-0``,  ``39.13-1``,  ``39.13-0``,  ``39.11-0``,  ``39.10-0``,  ``39.09-0``,  ``39.08-0``,  ``39.06-1``,  ``39.06-0``,  ``39.01-1``,  ``39.01-0``,  ``39.00-0``,  ``38.99-0``,  ``38.98-1``,  ``38.98-0``,  ``38.97-1``,  ``38.97-0``,  ``38.96-1``,  ``38.96-0``,  ``38.95-1``,  ``38.95-0``,  ``38.93-0``,  ``38.92-0``,  ``38.91-1``,  ``38.91-0``,  ``38.90-3``,  ``38.90-2``,  ``38.90-1``,  ``38.90-0``,  ``38.89-0``,  ``38.88-0``,  ``38.87-0``,  ``38.86-0``,  ``38.84-1``,  ``38.84-0``,  ``38.79-0``,  ``38.76-0``,  ``38.75-0``,  ``38.73-0``,  ``38.72-0``,  ``38.71-0``,  ``38.70-0``,  ``38.69-0``,  ``38.68-0``,  ``38.67-0``,  ``38.65-0``,  ``38.63-0``,  ``38.62-0``,  ``38.61b-0``,  ``38.58-0``,  ``38.57-0``,  ``38.56-0``,  ``38.51-0``,  ``38.49-0``,  ``38.46-0``,  ``38.45-0``,  ``38.44-0``,  ``38.22-1``,  ``38.22-0``,  ``38.20-0``,  ``38.19-0``,  ``38.18-0``,  ``38.16-0``,  ``38.06-2``,  ``38.06-0``,  ``37.99-1``,  ``37.99-0``,  ``37.96-0``,  ``37.95-0``,  ``37.90-0``,  ``37.78-0``,  ``37.77-0``,  ``37.75-0``,  ``37.66-0``,  ``37.62-2``,  ``37.62-1``,  ``37.62-0``,  ``37.52-1``,  ``37.52-0``,  ``37.17-1``,  ``37.17-0``,  ``37.10-1``,  ``37.10-0``,  ``37.02-0``,  ``36.84-0``,  ``36.32-0``,  ``35.85-2``,  ``35.85-1``
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:depends on bzip2: ``>=1.0.8,<2.0a0``
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:depends on samtools: ``>=1.22.1,<2.0a0``
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:depends on samtools: ``>=1.23.1,<2.0a0``
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‎_sources/recipes/bioconductor-dada2/README.rst.txt‎

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<details><summary><span class="truncated-version-list"><code>1.38.0-0</code>,  <code>1.34.0-2</code>,  <code>1.34.0-1</code>,  <code>1.34.0-0</code>,  <code>1.30.0-0</code>,  <code>1.28.0-0</code>,  <code>1.26.0-1</code>,  <code>1.26.0-0</code>,  <code>1.22.0-2</code>,  </span></summary>
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``1.38.0-0``,  ``1.34.0-2``,  ``1.34.0-1``,  ``1.34.0-0``,  ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-1``,  ``1.26.0-0``,  ``1.22.0-2``,  ``1.22.0-1``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-1``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.1-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.4-0``,  ``1.4.0-0``,  ``1.2-0``,  ``1.0.3-0``,  ``0.99.10-0``,  ``0.10.4-0``,  ``0.10.3-0``,  ``0.10.1-0``,  ``0.10.0-0``
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``1.38.0-0``,  ``1.34.0-2``,  ``1.34.0-1``,  ``1.34.0-0``,  ``1.30.0-0``,  ``1.28.0-0``,  ``1.26.0-1``,  ``1.26.0-0``,  ``1.22.0-2``,  ``1.22.0-1``,  ``1.22.0-0``,  ``1.20.0-0``,  ``1.18.0-1``,  ``1.18.0-0``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.1-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.4.0-0``,  ``1.4-0``,  ``1.2-0``,  ``1.0.3-0``,  ``0.99.10-0``,  ``0.10.4-0``,  ``0.10.3-0``,  ``0.10.1-0``,  ``0.10.0-0``
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‎_sources/recipes/caalm/README.rst.txt‎

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:orphan: .. only available via index, not via toctree
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.. title:: Package Recipe 'caalm'
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.. highlight: bash
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caalm
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=====
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.. conda:recipe:: caalm
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:replaces_section_title:
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:noindex:
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Carbohydrate Activity Annotation with protein Language Models
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:homepage: https://github.com/lczong/CAALM
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:license: Apache-2.0
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:recipe: /`caalm <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/caalm>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/caalm/meta.yaml>`_
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.. conda:package:: caalm
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|downloads_caalm| |docker_caalm|
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:versions:
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``1.0.0-0``
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:depends on biopython: ``>=1.86``
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:depends on faiss-cpu:
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:depends on jinja2: ``>=3.1``
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:depends on markupsafe: ``>=2.0``
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:depends on numpy: ``>=1.26``
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:depends on python: ``>=3.10``
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:depends on pytorch: ``>=2.6.0``
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:depends on pyyaml: ``>=6.0``
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:depends on tqdm: ``>=4.67``
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:depends on transformers: ``>=4.55.0,<5``
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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 caalm
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to add into an existing workspace instead, run::
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pixi add caalm
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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 caalm
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Alternatively, to install into a new environment, run::
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conda create -n envname caalm
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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/caalm:<tag>
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(see `caalm/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_caalm| image:: https://img.shields.io/conda/dn/bioconda/caalm.svg?style=flat
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:target: https://anaconda.org/bioconda/caalm
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:alt: (downloads)
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.. |docker_caalm| image:: https://quay.io/repository/biocontainers/caalm/status
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:target: https://quay.io/repository/biocontainers/caalm
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.. _`caalm/tags`: https://quay.io/repository/biocontainers/caalm?tab=tags
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.. raw:: html
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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/caalm/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/caalm/README.html

‎_sources/recipes/cellitac/README.rst.txt‎

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‎_sources/recipes/clipkit/README.rst.txt‎

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<details><summary><span class="truncated-version-list"><code>2.11.4-0</code>,  <code>2.10.2-0</code>,  <code>2.7.0-0</code>,  <code>2.6.1-0</code>,  <code>2.4.1-0</code>,  <code>2.4.0-0</code>,  <code>2.3.0-0</code>,  <code>2.2.6-0</code>,  <code>2.2.5-0</code>,  </span></summary>
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<details><summary><span class="truncated-version-list"><code>2.12.0-0</code>,  <code>2.11.4-0</code>,  <code>2.10.2-0</code>,  <code>2.7.0-0</code>,  <code>2.6.1-0</code>,  <code>2.4.1-0</code>,  <code>2.4.0-0</code>,  <code>2.3.0-0</code>,  <code>2.2.6-0</code>,  </span></summary>
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``2.11.4-0``,  ``2.10.2-0``,  ``2.7.0-0``,  ``2.6.1-0``,  ``2.4.1-0``,  ``2.4.0-0``,  ``2.3.0-0``,  ``2.2.6-0``,  ``2.2.5-0``,  ``2.2.4-0``,  ``2.2.2-0``,  ``2.2.0-0``,  ``2.1.3-0``,  ``2.1.2-0``,  ``2.1.1-0``,  ``2.1.0-0``,  ``2.0.1-0``,  ``1.4.1-0``,  ``1.3.0-0``,  ``1.2.0-0``,  ``1.1.6-0``,  ``1.1.5-0``,  ``1.1.3-0``,  ``1.1.1-0``,  ``1.1.0-0``,  ``1.0.7-0``,  ``1.0.4-0``,  ``1.0.3-0``,  ``0.2.0-0``,  ``0.1.9-0``,  ``0.1.3-0``,  ``0.1.2-0``
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``2.12.0-0``,  ``2.11.4-0``,  ``2.10.2-0``,  ``2.7.0-0``,  ``2.6.1-0``,  ``2.4.1-0``,  ``2.4.0-0``,  ``2.3.0-0``,  ``2.2.6-0``,  ``2.2.5-0``,  ``2.2.4-0``,  ``2.2.2-0``,  ``2.2.0-0``,  ``2.1.3-0``,  ``2.1.2-0``,  ``2.1.1-0``,  ``2.1.0-0``,  ``2.0.1-0``,  ``1.4.1-0``,  ``1.3.0-0``,  ``1.2.0-0``,  ``1.1.6-0``,  ``1.1.5-0``,  ``1.1.3-0``,  ``1.1.1-0``,  ``1.1.0-0``,  ``1.0.7-0``,  ``1.0.4-0``,  ``1.0.3-0``,  ``0.2.0-0``,  ``0.1.9-0``,  ``0.1.3-0``,  ``0.1.2-0``
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<script>
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var package = "clipkit";
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var versions = ["2.12.0","2.11.4","2.10.2","2.7.0","2.6.1"];
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‎_sources/recipes/comet-ms/README.rst.txt‎

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.. raw:: html
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<details><summary><span class="truncated-version-list"><code>2024011-0</code>,  <code>2023012-1</code>,  <code>2023012-0</code>,  <code>2023010-2</code>,  <code>2023010-1</code>,  <code>2023010-0</code>,  <code>2021010-1</code>,  <code>2021010-0</code>,  <code>2019015-0</code>,  </span></summary>
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<details><summary><span class="truncated-version-list"><code>2026011-0</code>,  <code>2024011-0</code>,  <code>2023012-1</code>,  <code>2023012-0</code>,  <code>2023010-2</code>,  <code>2023010-1</code>,  <code>2023010-0</code>,  <code>2021010-1</code>,  <code>2021010-0</code>,  </span></summary>
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``2024011-0``,  ``2023012-1``,  ``2023012-0``,  ``2023010-2``,  ``2023010-1``,  ``2023010-0``,  ``2021010-1``,  ``2021010-0``,  ``2019015-0``,  ``2019014-0``,  ``2019013-0``,  ``2019012-0``,  ``2019011-0``,  ``2019010-0``,  ``2018014-0``,  ``2018013-0``,  ``2018012-1``,  ``2018012-0``,  ``2016013-7``,  ``2016013-6``,  ``2016013-5``,  ``2016013-4``,  ``2016013-3``,  ``2016013-2``,  ``2016013-1``,  ``2026.01.1-0``
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``2026011-0``,  ``2024011-0``,  ``2023012-1``,  ``2023012-0``,  ``2023010-2``,  ``2023010-1``,  ``2023010-0``,  ``2021010-1``,  ``2021010-0``,  ``2019015-0``,  ``2019014-0``,  ``2019013-0``,  ``2019012-0``,  ``2019011-0``,  ``2019010-0``,  ``2018014-0``,  ``2018013-0``,  ``2018012-1``,  ``2018012-0``,  ``2016013-7``,  ``2016013-6``,  ``2016013-5``,  ``2016013-4``,  ``2016013-3``,  ``2016013-2``,  ``2016013-1``,  ``2026.01.1-0``
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:depends on __glibc: ``>=2.17,<3.0.a0``
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:depends on libgcc-ng: ``>=12``
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:depends on libstdcxx-ng: ``>=12``
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:additional platforms:
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‎_sources/recipes/ezcharts/README.rst.txt‎

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eCharts plotting API.
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:homepage: https://github.com/epi2me-labs/ezcharts
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:documentation: https://github.com/epi2me-labs/ezcharts/blob/v0.16.1/README.md
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:license: BSD / BSD-4-Clause
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:recipe: /`ezcharts <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/ezcharts>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/ezcharts/meta.yaml>`_
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``0.15.2-0``,  ``0.15.1-0``,  ``0.15.0-0``,  ``0.14.1-0``,  ``0.14.0-0``,  ``0.13.1-0``,  ``0.11.2-0``,  ``0.10.2-0``
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``0.16.1-0``,  ``0.15.2-0``,  ``0.15.1-0``,  ``0.15.0-0``,  ``0.14.1-0``,  ``0.14.0-0``,  ``0.13.1-0``,  ``0.11.2-0``,  ``0.10.2-0``
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var versions = ["0.16.1","0.15.2","0.15.1","0.15.0","0.14.1"];
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