recipe saccharis

A CAZyme discovery tool. Easily create phylogenetic trees from FASTA files and CAZyme families.

Homepage:

https://github.com/saccharis/SACCHARIS_2

License:

GPL3 / GPL-3.0-or-later

Recipe:

/saccharis/meta.yaml

Bioinformatics pipeline to automate phylogenetic analysis of CAZyme families in FASTA sequences via creation of phylogenetic trees.

package saccharis

versions:

2.0.1-1,  2.0.1-0,  2.0.1.dev21-9,  2.0.1.dev21-8,  2.0.1.dev21-7,  2.0.1.dev21-6,  2.0.1.dev21-5,  2.0.1.dev21-4,  2.0.1.dev21-3, 

2.0.1-1,  2.0.1-0,  2.0.1.dev21-9,  2.0.1.dev21-8,  2.0.1.dev21-7,  2.0.1.dev21-6,  2.0.1.dev21-5,  2.0.1.dev21-4,  2.0.1.dev21-3,  2.0.1.dev21-2,  2.0.1.dev21-0,  2.0.0.dev21-2,  2.0.0.dev21-0,  2.0.0.dev20-0,  2.0.0.dev19-7,  2.0.0.dev19-0,  2.0.0.dev18-0

depends beautifulsoup4:

>=4.11.1

depends biopython:

>=1.79

depends blast:

>=2.*

depends dbcan:

<4

depends diamond:

>=2.0.15

depends fasttree:

>=2.1.11

depends hmmer:

>=3.3

depends lxml:

>=4.9.0

depends modeltest-ng:

>=0.1.7

depends muscle:

>=3.8

depends ncbi-datasets-pylib:

>=14.*

depends psutil:

depends pyqt:

>=5,<6

depends pyqt5-sip:

>=12.11

depends python:

>=3.8

depends python-dotenv:

>=0.20.0

depends python-wget:

>=3.2

depends raxml:

>=8.2.12

depends raxml-ng:

>=1.2

depends requests:

>=2.28.0

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 saccharis

and update with::

   mamba update saccharis

To create a new environment, run:

mamba create --name myenvname saccharis

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/saccharis:<tag>

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

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/saccharis/README.html)