recipe transit

TRANSIT

Homepage:

http://github.com/mad-lab/transit

Developer docs:

https://github.com/simongog/sdsl-lite

License:

GPL / GPL-3

Recipe:

/transit/meta.yaml

TRANSIT is a software that can be used to analyze Tn-Seq datasets. It includes various statistical calculations of essentiality of genes or genomic regions (including conditional essentiality between 2 conditions).

package transit

versions:

3.2.3-0,  3.2.2-0,  3.2.1-0,  3.2.0-0,  3.1.0-0,  3.0.2-1,  3.0.2-0,  3.0.1-0,  2.5.2-0, 

3.2.3-0,  3.2.2-0,  3.2.1-0,  3.2.0-0,  3.1.0-0,  3.0.2-1,  3.0.2-0,  3.0.1-0,  2.5.2-0,  2.3.3-1,  2.3.3-0,  2.3.2-0,  2.3.1-0

depends matplotlib-base:

>=3,<3.1

depends numpy:

>=1.16,<1.17

depends pillow:

>=6,<6.1

depends python:

>=3.6

depends scipy:

>=1.2,<1.3

depends statsmodels:

>=0.9,<0.10

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 transit

and update with::

   mamba update transit

To create a new environment, run:

mamba create --name myenvname transit

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/transit:<tag>

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

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