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‎_sources/recipes/amaranth-assembler/README.rst.txt‎

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:orphan: .. only available via index, not via toctree
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.. title:: Package Recipe 'amaranth-assembler'
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.. highlight: bash
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amaranth-assembler
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==================
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.. conda:recipe:: amaranth-assembler
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:replaces_section_title:
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:noindex:
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Amaranth is a reference\-based transcriptome assembler for single\-cell RNA\-seq.
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:homepage: https://github.com/Shao-Group/amaranth
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:license: BSD / BSD-3-Clause
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:recipe: /`amaranth-assembler <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/amaranth-assembler>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/amaranth-assembler/meta.yaml>`_
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.. conda:package:: amaranth-assembler
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|downloads_amaranth-assembler| |docker_amaranth-assembler|
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:versions:
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``0.1.0-0``
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:depends _openmp_mutex: ``>=4.5``
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:depends htslib: ``>=1.22.1,<1.23.0a0``
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:depends libgcc: ``>=13``
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:depends libstdcxx: ``>=13``
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:depends libxcrypt: ``>=4.4.36``
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:depends libzlib: ``>=1.3.1,<2.0a0``
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:requirements:
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:additional platforms:
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.. raw:: html
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<span class="additional-platforms"><code>linux-aarch64</code>,  <code>osx-arm64</code></span>
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.. rubric:: Installation
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You need a conda-compatible package manager
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(currently either `micromamba <https://mamba.readthedocs.io>`_, `mamba <https://mamba.readthedocs.io>`_, or `conda <https://docs.conda.io/projects/conda>`_)
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and the Bioconda channel already activated (see :ref:`set-up-channels`).
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While any of above package managers is fine, it is currently recommended to use either
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micromamba or mamba (see `here <https://mamba.readthedocs.io>`_ for installation instructions).
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We will show all commands using mamba below, but the arguments are the same for the two
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others.
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Given that you already have a conda environment in which you want to have this package, install with::
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mamba install amaranth-assembler
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and update with::
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mamba update amaranth-assembler
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To create a new environment, run::
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mamba create --name myenvname amaranth-assembler
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with ``myenvname`` being a reasonable name for the environment
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(see e.g. the `mamba docs <https://mamba.readthedocs.io>`_ for details and further options).
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Alternatively, use the docker container::
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docker pull quay.io/biocontainers/amaranth-assembler:<tag>
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(see `amaranth-assembler/tags`_ for valid values for ``<tag>``)
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.. |downloads_amaranth-assembler| image:: https://img.shields.io/conda/dn/bioconda/amaranth-assembler.svg?style=flat
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:target: https://anaconda.org/bioconda/amaranth-assembler
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:alt: (downloads)
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.. |docker_amaranth-assembler| image:: https://quay.io/repository/biocontainers/amaranth-assembler/status
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:target: https://quay.io/repository/biocontainers/amaranth-assembler
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.. _`amaranth-assembler/tags`: https://quay.io/repository/biocontainers/amaranth-assembler?tab=tags
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.. raw:: html
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<script>
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var package = "amaranth-assembler";
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var versions = ["0.1.0"];
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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/amaranth-assembler/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/amaranth-assembler/README.html

‎_sources/recipes/ampliconsuite/README.rst.txt‎

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.. raw:: html
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<details><summary><span class="truncated-version-list"><code>1.4.0-0</code>,  <code>1.3.9-0</code>,  <code>1.3.8-0</code>,  <code>1.3.7-0</code>,  <code>1.3.6-0</code>,  <code>1.3.5-0</code>,  <code>1.3.4-0</code>,  <code>1.3.3-0</code>,  <code>1.3.2-0</code>,  </span></summary>
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<details><summary><span class="truncated-version-list"><code>1.5.0-0</code>,  <code>1.4.0-0</code>,  <code>1.3.9-0</code>,  <code>1.3.8-0</code>,  <code>1.3.7-0</code>,  <code>1.3.6-0</code>,  <code>1.3.5-0</code>,  <code>1.3.4-0</code>,  <code>1.3.3-0</code>,  </span></summary>
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``1.4.0-0``,  ``1.3.9-0``,  ``1.3.8-0``,  ``1.3.7-0``,  ``1.3.6-0``,  ``1.3.5-0``,  ``1.3.4-0``,  ``1.3.3-0``,  ``1.3.2-0``,  ``1.3.1-0``,  ``1.2.2-0``,  ``1.2.1-0``,  ``1.2.0-0``,  ``1.1.3-0``,  ``1.1.2-0``,  ``1.1.1-0``,  ``1.1.0-0``,  ``1.0.0-0``,  ``0.1555.2-1``,  ``0.1555.2-0``
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``1.5.0-0``,  ``1.4.0-0``,  ``1.3.9-0``,  ``1.3.8-0``,  ``1.3.7-0``,  ``1.3.6-0``,  ``1.3.5-0``,  ``1.3.4-0``,  ``1.3.3-0``,  ``1.3.2-0``,  ``1.3.1-0``,  ``1.2.2-0``,  ``1.2.1-0``,  ``1.2.0-0``,  ``1.1.3-0``,  ``1.1.2-0``,  ``1.1.1-0``,  ``1.1.0-0``,  ``1.0.0-0``,  ``0.1555.2-1``,  ``0.1555.2-0``
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<script>
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var package = "ampliconsuite";
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var versions = ["1.4.0","1.3.9","1.3.8","1.3.7","1.3.6"];
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var versions = ["1.5.0","1.4.0","1.3.9","1.3.8","1.3.7"];
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</script>
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‎_sources/recipes/arborist/README.rst.txt‎

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:orphan: .. only available via index, not via toctree
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.. title:: Package Recipe 'arborist'
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.. highlight: bash
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arborist
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========
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.. conda:recipe:: arborist
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:replaces_section_title:
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:noindex:
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Arborist is a tool to rank SNV phylogenies inferred from bulk DNA sequencing via scDNA\-seq data
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:homepage: https://github.com/VanLoo-lab/Arborist
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:license: BSD-3-Clause
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:recipe: /`arborist <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/arborist>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/arborist/meta.yaml>`_
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.. conda:package:: arborist
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|downloads_arborist| |docker_arborist|
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:versions:
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``1.0.0-0``
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:depends networkx: ``>=3.6``
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:depends numba: ``>=0.61,<0.62``
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:depends numpy: ``>=1.26``
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:depends pandas: ``>=1.3,<3.0``
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:depends pygraphviz:
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:depends python: ``>=3.7``
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:depends scipy: ``>=1.7``
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:requirements:
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:additional platforms:
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.. rubric:: Installation
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You need a conda-compatible package manager
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(currently either `micromamba <https://mamba.readthedocs.io>`_, `mamba <https://mamba.readthedocs.io>`_, or `conda <https://docs.conda.io/projects/conda>`_)
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and the Bioconda channel already activated (see :ref:`set-up-channels`).
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While any of above package managers is fine, it is currently recommended to use either
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micromamba or mamba (see `here <https://mamba.readthedocs.io>`_ for installation instructions).
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We will show all commands using mamba below, but the arguments are the same for the two
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others.
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Given that you already have a conda environment in which you want to have this package, install with::
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mamba install arborist
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and update with::
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mamba update arborist
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To create a new environment, run::
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mamba create --name myenvname arborist
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with ``myenvname`` being a reasonable name for the environment
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(see e.g. the `mamba docs <https://mamba.readthedocs.io>`_ for details and further options).
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Alternatively, use the docker container::
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docker pull quay.io/biocontainers/arborist:<tag>
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(see `arborist/tags`_ for valid values for ``<tag>``)
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.. |downloads_arborist| image:: https://img.shields.io/conda/dn/bioconda/arborist.svg?style=flat
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:target: https://anaconda.org/bioconda/arborist
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:alt: (downloads)
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.. |docker_arborist| image:: https://quay.io/repository/biocontainers/arborist/status
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:target: https://quay.io/repository/biocontainers/arborist
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.. _`arborist/tags`: https://quay.io/repository/biocontainers/arborist?tab=tags
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.. raw:: html
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<script>
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var package = "arborist";
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var versions = ["1.0.0"];
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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/arborist/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/arborist/README.html

‎_sources/recipes/atol-qc-annotation/README.rst.txt‎

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:orphan: .. only available via index, not via toctree
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.. title:: Package Recipe 'atol-qc-annotation'
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.. highlight: bash
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atol-qc-annotation
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==================
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.. conda:recipe:: atol-qc-annotation
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:replaces_section_title:
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:noindex:
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Run QC on GTF and GFF files.
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:homepage: https://github.com/TomHarrop/atol-qc-annotation
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:license: GPL3 / GPL-3.0-or-later
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:recipe: /`atol-qc-annotation <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/atol-qc-annotation>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/atol-qc-annotation/meta.yaml>`_
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.. conda:package:: atol-qc-annotation
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|downloads_atol-qc-annotation| |docker_atol-qc-annotation|
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:versions:
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``0.1.0-0``
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:depends agat: ``>=1.5.1``
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:depends bbmap: ``>=39.52``
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:depends busco: ``>=5.8.3,<6``
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:depends omark: ``>=0.3.1``
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:depends pytables: ``>=3.10.2``
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:depends python: ``>=3.12,<3.13``
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:depends snakemake: ``>=9.11.6,<10``
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:requirements:
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:additional platforms:
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.. rubric:: Installation
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You need a conda-compatible package manager
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(currently either `micromamba <https://mamba.readthedocs.io>`_, `mamba <https://mamba.readthedocs.io>`_, or `conda <https://docs.conda.io/projects/conda>`_)
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and the Bioconda channel already activated (see :ref:`set-up-channels`).
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While any of above package managers is fine, it is currently recommended to use either
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micromamba or mamba (see `here <https://mamba.readthedocs.io>`_ for installation instructions).
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We will show all commands using mamba below, but the arguments are the same for the two
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others.
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Given that you already have a conda environment in which you want to have this package, install with::
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mamba install atol-qc-annotation
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and update with::
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mamba update atol-qc-annotation
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To create a new environment, run::
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mamba create --name myenvname atol-qc-annotation
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with ``myenvname`` being a reasonable name for the environment
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(see e.g. the `mamba docs <https://mamba.readthedocs.io>`_ for details and further options).
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Alternatively, use the docker container::
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docker pull quay.io/biocontainers/atol-qc-annotation:<tag>
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(see `atol-qc-annotation/tags`_ for valid values for ``<tag>``)
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.. |downloads_atol-qc-annotation| image:: https://img.shields.io/conda/dn/bioconda/atol-qc-annotation.svg?style=flat
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:target: https://anaconda.org/bioconda/atol-qc-annotation
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:alt: (downloads)
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.. |docker_atol-qc-annotation| image:: https://quay.io/repository/biocontainers/atol-qc-annotation/status
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:target: https://quay.io/repository/biocontainers/atol-qc-annotation
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.. _`atol-qc-annotation/tags`: https://quay.io/repository/biocontainers/atol-qc-annotation?tab=tags
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.. raw:: html
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<script>
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var package = "atol-qc-annotation";
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var versions = ["0.1.0"];
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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/atol-qc-annotation/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/atol-qc-annotation/README.html

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