recipe kallisto

Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

Homepage:

https://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: kallisto, doi: 10.1038/nbt.3519, usegalaxy-eu: kallisto_pseudo, usegalaxy-eu: kallisto_quant

package kallisto

(downloads) docker_kallisto

versions:
0.51.1-0,  0.51.0-0,  0.50.1-2,  0.50.1-1,  0.50.1-0,  0.50.0-0,  0.48.0-2,  0.48.0-1,  0.48.0-0, 

0.51.1-0,  0.51.0-0,  0.50.1-2,  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

depends bzip2:

>=1.0.8,<2.0a0

depends hdf5:

>=1.14.3,<1.14.4.0a0

depends libcurl:

>=8.8.0,<9.0a0

depends libgcc:

>=12

depends libstdcxx:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends xz:

>=5.2.6,<6.0a0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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:<tag>

(see `kallisto/tags`_ for valid values for ``<tag>``)

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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)