recipe cutadapt

Trim adapters from high-throughput sequencing reads

Homepage:

https://cutadapt.readthedocs.io/

Developer docs:

https://github.com/marcelm/cutadapt

License:

MIT / MIT

Recipe:

/cutadapt/meta.yaml

Links:

biotools: cutadapt, doi: 10.14806/ej.17.1.200, usegalaxy-eu: cutadapt

package cutadapt

versions:

5.0-0,  4.9-3,  4.9-2,  4.9-1,  4.9-0,  4.8-1,  4.8-0,  4.7-1,  4.7-0, 

5.0-0,  4.9-3,  4.9-2,  4.9-1,  4.9-0,  4.8-1,  4.8-0,  4.7-1,  4.7-0,  4.6-2,  4.6-1,  4.6-0,  4.5-0,  4.4-1,  4.4-0,  4.3-0,  4.2-0,  4.1-1,  4.1-0,  4.0-0,  3.7-1,  3.7-0,  3.6-0,  3.5-1,  3.5-0,  3.4-1,  3.4-0,  3.3-1,  3.3-0,  3.2-0,  3.1-0,  3.0-0,  2.10-1,  2.10-0,  2.9-0,  2.8-0,  2.7-0,  2.6-0,  2.5-0,  2.4-0,  2.3-0,  2.2-0,  2.1-0,  2.0-0,  1.18-1,  1.18-0,  1.17-0,  1.16-2,  1.16-1,  1.16-0,  1.15-0,  1.14-0,  1.13-0,  1.12-1,  1.12-0,  1.11-0,  1.10-0,  1.9.1-0,  1.8.3-0,  1.8.1-0

depends dnaio:

>=1.2.2

depends libgcc:

>=13

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends xopen:

>=1.6.0

requirements:

additional platforms:

linux-aarch64,  osx-arm64

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 cutadapt

and update with::

   mamba update cutadapt

To create a new environment, run:

mamba create --name myenvname cutadapt

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/cutadapt:<tag>

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

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