recipe daisysuite

DaisySuite - mapping-based pipeline for horizontal gene transfer (HGT) detection using sequencing data

Homepage:

https://gitlab.com/eseiler/DaisySuite

License:

GNU GPLv3

Recipe:

/daisysuite/meta.yaml

package daisysuite

versions:

1.3.0-2,  1.3.0-1,  1.3.0-0,  1.2.1-1,  1.2.1-0,  1.2.0-1,  1.2.0-0,  1.1.0-0,  1.0.0-0

depends bedtools:

2.22

depends biopython:

1.72

depends bwa:

0.7.12

depends clever-toolkit:

2.0rc3

depends gustaf:

1.0.8

depends mason:

2.0.7

depends pandas:

0.18.1

depends pysam:

0.9.1.4

depends sak:

0.4.6

depends samtools:

1.9

depends scipy:

1.1.0

depends snakemake:

3.9.0

depends stellar:

1.4.9

depends yara:

0.9.6

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 daisysuite

and update with::

   mamba update daisysuite

To create a new environment, run:

mamba create --name myenvname daisysuite

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/daisysuite:<tag>

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

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