:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'kallisto' .. highlight: bash kallisto ======== .. conda:recipe:: kallisto :replaces_section_title: :noindex: Quantifying abundances of transcripts from RNA\-Seq data\, or more generally of target sequences using high\-throughput sequencing reads. :homepage: http://pachterlab.github.io/kallisto :documentation: https://pachterlab.github.io/kallisto/manual.html :developer docs: https://github.com/pachterlab/kallisto :license: BSD / BSD-2-Clause :recipe: /`kallisto `_/`meta.yaml `_ :links: biotools: :biotools:`kallisto`, doi: :doi:`10.1038/nbt.3519` .. conda:package:: kallisto |downloads_kallisto| |docker_kallisto| :versions: .. raw:: html
0.50.1-10.50.1-00.50.0-00.48.0-20.48.0-10.48.0-00.46.2-20.46.2-10.46.2-0 ``0.50.1-1``,  ``0.50.1-0``,  ``0.50.0-0``,  ``0.48.0-2``,  ``0.48.0-1``,  ``0.48.0-0``,  ``0.46.2-2``,  ``0.46.2-1``,  ``0.46.2-0``,  ``0.46.1-0``,  ``0.46.0-1``,  ``0.46.0-0``,  ``0.45.1-0``,  ``0.45.0-0``,  ``0.44.0-2``,  ``0.44.0-1``,  ``0.43.1-1``,  ``0.43.1-0``,  ``0.43.0-2``,  ``0.43.0-1``,  ``0.42.4-2``,  ``0.42.4-1``,  ``0.42.3-1``,  ``0.42.3-0`` .. raw:: html
:depends bzip2: ``>=1.0.8,<2.0a0`` :depends hdf5: ``>=1.12.2,<1.12.3.0a0`` :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends xz: ``>=5.2.6,<6.0a0`` :depends zlib: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 kallisto and update with:: mamba update kallisto To create a new environment, run:: mamba create --name myenvname kallisto 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/kallisto: (see `kallisto/tags`_ for valid values for ````) .. |downloads_kallisto| image:: https://img.shields.io/conda/dn/bioconda/kallisto.svg?style=flat :target: https://anaconda.org/bioconda/kallisto :alt: (downloads) .. |docker_kallisto| image:: https://quay.io/repository/biocontainers/kallisto/status :target: https://quay.io/repository/biocontainers/kallisto .. _`kallisto/tags`: https://quay.io/repository/biocontainers/kallisto?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html 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/kallisto/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/kallisto/README.html