recipe ipyrad

Interactive assembly and analysis of RAD-seq data sets.

Homepage:

http://github.com/dereneaton/ipyrad

License:

GPL3 / GPL-3.0-only

Recipe:

/ipyrad/meta.yaml

package ipyrad

(downloads) docker_ipyrad

versions:
0.9.105-0,  0.9.104-0,  0.9.103-0,  0.9.102-0,  0.9.101-0,  0.9.100-0,  0.9.99-0,  0.9.98-0,  0.9.97-0, 

0.9.105-0,  0.9.104-0,  0.9.103-0,  0.9.102-0,  0.9.101-0,  0.9.100-0,  0.9.99-0,  0.9.98-0,  0.9.97-0,  0.9.96-0,  0.9.95-0,  0.9.94-0,  0.9.93-0,  0.9.92-0,  0.9.90-0,  0.9.89-0,  0.9.88-0,  0.9.87-0,  0.9.86-0,  0.9.85-0,  0.9.84-1,  0.9.84-0,  0.9.82-0,  0.9.81-0,  0.9.80-0,  0.9.78-0,  0.9.77-0,  0.9.74-0,  0.9.71-0,  0.9.68-0,  0.9.67-0,  0.9.66-0,  0.9.65-0,  0.9.64-0,  0.9.63-0,  0.9.62-0,  0.9.61-0,  0.9.60-0,  0.9.59-0,  0.9.58-0,  0.9.57-0,  0.9.56-1,  0.9.56-0,  0.9.54-0,  0.9.53-0,  0.9.52-0,  0.9.51-0,  0.9.50-0,  0.9.49-0,  0.9.48-0,  0.9.47-0,  0.9.46-0,  0.9.45-0,  0.9.44-0,  0.9.43-0,  0.9.42-0,  0.9.41-0,  0.9.40-0,  0.9.33-0,  0.9.32-0,  0.9.31-0,  0.9.30-0,  0.9.29-0,  0.9.28-0,  0.9.26-0,  0.9.25-0,  0.9.24-0,  0.9.20-0,  0.9.19-1,  0.9.19-0,  0.9.18-0,  0.9.17-0,  0.9.16-0,  0.9.15-0,  0.9.14-0,  0.9.13-0,  0.9.12-0,  0.9.11-1,  0.9.11-0,  0.9.10-0,  0.9.8-0,  0.9.7-0

depends bedtools:

depends bwa:

depends cutadapt:

depends future:

depends h5py:

depends ipyparallel:

>=6.0.2

depends mpi4py:

>=3.0

depends muscle:

<5

depends notebook:

depends numba:

>=0.37

depends numpy:

depends pandas:

depends pysam:

>=0.15

depends python:

depends requests:

depends samtools:

depends scipy:

depends toyplot:

depends vsearch:

>=2.13

requirements:

additional platforms:

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 ipyrad

and update with::

   mamba update ipyrad

To create a new environment, run:

mamba create --name myenvname ipyrad

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/ipyrad:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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