recipe sphae

Phage toolkit

Homepage:

https://github.com/linsalrob/sphae/

Documentation:

https://github.com/linsalrob/sphae

Developer docs:

https://github.com/linsalrob/sphae

License:

MIT / MIT

Recipe:

/sphae/meta.yaml

Assembling and annotating pure culture phages from both Illumina and Nanopore sequencing technology

package sphae

versions:

1.4.5-0,  1.4.4-0,  1.4.3-0,  1.4.2-0,  1.4.1-0,  1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3.1-0, 

1.4.5-0,  1.4.4-0,  1.4.3-0,  1.4.2-0,  1.4.1-0,  1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3.1-0,  1.3.1b-0

depends attrmap:

>=0.0.7

depends biopython:

>=1.8.1

depends click:

>=8.1.3

depends jinja2:

>=3.0.2

depends metasnek:

>=0.0.4

depends pandas:

depends python:

<3.12

depends pyyaml:

>=6.0

depends snakemake-minimal:

>=7.14.0

depends snaketool-utils:

>=0.0.4

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 sphae

and update with::

   mamba update sphae

To create a new environment, run:

mamba create --name myenvname sphae

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/sphae:<tag>

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

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