recipe seqstr

Lightweight tool to compile simple string input into long genomic sequences

Homepage:

https://github.com/jzhoulab/Seqstr

License:

MIT

Recipe:

/seqstr/meta.yaml

Seqstr is designed to provide a concise and flexible way to specify long genomic sequences that can be used for downstream analysis. For example, it can be used by web servers to avoid transferring long genomic sequences. Seqstr is also a format specification, which can be implemented in different languages. We also provide a test suite for verifying an implementation.

package seqstr

(downloads) docker_seqstr

versions:

0.1.0-0

depends pyfaidx:

>=0.6.3

depends python:

>=3.7

depends requests:

>=2.25.0

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 seqstr

and update with::

   mamba update seqstr

To create a new environment, run:

mamba create --name myenvname seqstr

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/seqstr:<tag>

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

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