recipe jaeger-bio

A quick and precise pipeline for detecting phages in sequence assemblies.

Homepage:

https://github.com/Yasas1994/Jaeger

Documentation:

https://readthedocs.org/projects/jaeger-docs/

License:

MIT / MIT

Recipe:

/jaeger-bio/meta.yaml

Links:

biotools: jaeger

package jaeger-bio

versions:

1.1.26-0

depends biopython:

>=1.78

depends h5py:

>=3.8

depends kneed:

>=0.8.5

depends matplotlib-base:

>=3.7

depends numpy:

>=1.24

depends pandas:

>=1.5

depends parasail-python:

>=1.3.4

depends pip:

depends psutil:

>=5

depends python:

3.*

depends ruptures:

>=1.1.9

depends scikit-learn:

1.3.2

depends seaborn:

>=0.12.2

depends tensorflow:

>=2.15,<2.16

depends tqdm:

>=4.64.0

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 jaeger-bio

and update with::

   mamba update jaeger-bio

To create a new environment, run:

mamba create --name myenvname jaeger-bio

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/jaeger-bio:<tag>

(see `jaeger-bio/tags`_ for valid values for ``<tag>``)

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