recipe chorus2

A pipeline to select oligonucleotides for fluorescence in situ hbridization (Oligo-FISH).

Homepage:

https://github.com/zhangtaolab/Chorus2

Documentation:

https://chorus2.readthedocs.io/en/dev/

License:

MIT license

Recipe:

/chorus2/meta.yaml

Links:

biotools: chorus2

package chorus2

versions:

2.01-2,  2.01-1,  2.01-0,  2.0.1-0,  2.0-5,  2.0-4,  2.0-3,  2.0-2,  2.0-1, 

2.01-2,  2.01-1,  2.01-0,  2.0.1-0,  2.0-5,  2.0-4,  2.0-3,  2.0-2,  2.0-1,  2.0-0

depends bcftools:

depends bwa:

>=0.7.3a,<=0.7.8

depends kmer-jellyfish:

2.*

depends matplotlib-base:

>=3

depends numpy:

depends pandas:

depends primer3-py:

>=0.4.2

depends pybedtools:

depends pybigwig:

depends pyfasta:

depends pyqt:

<5.11

depends python:

>=3.9,<3.10.0a0

depends python_abi:

3.9.* *_cp39

depends samtools:

depends sip:

>=4

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 chorus2

and update with::

   mamba update chorus2

To create a new environment, run:

mamba create --name myenvname chorus2

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/chorus2:<tag>

(see `chorus2/tags`_ for valid values for ``<tag>``)

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