recipe tobias

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

Homepage:

https://github.com/loosolab/TOBIAS

Documentation:

https://github.com/loosolab/TOBIAS/wiki

License:

MIT / MIT

Recipe:

/tobias/meta.yaml

Links:

biotools: TOBIAS, doi: 10.1038/s41467-020-18035-1

TOBIAS (Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal) is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data.

package tobias

versions:

0.17.1-0,  0.17.0-1,  0.17.0-0,  0.16.1-1,  0.16.1-0,  0.16.0-0,  0.15.1-0,  0.13.3-1,  0.13.3-0, 

0.17.1-0,  0.17.0-1,  0.17.0-0,  0.16.1-1,  0.16.1-0,  0.16.0-0,  0.15.1-0,  0.13.3-1,  0.13.3-0,  0.13.2-1,  0.13.2-0,  0.13.1-0,  0.13.0-0,  0.12.12-0,  0.12.11-0,  0.12.10-1,  0.12.10-0,  0.12.9-0,  0.12.8-0,  0.12.7-0,  0.12.6-0,  0.12.4-0,  0.12.3-0,  0.12.1-0,  0.12.0-0,  0.11.6-1,  0.11.6-0,  0.11.4-0,  0.11.3-0,  0.11.2-0,  0.11.1-0,  0.11.0-0,  0.9.0-0,  0.8.0-0,  0.7.0-0,  0.6.4-0,  0.6.1-0,  0.5.0-0

depends adjusttext:

depends boto3:

depends importlib-metadata:

depends kneed:

depends libgcc:

>=13

depends logomaker:

depends matplotlib-base:

>=2

depends moods:

depends numpy:

>=1.22.4,<2.0a0

depends pandas:

depends pybedtools:

depends pybigwig:

>=0.3

depends pypdf2:

depends pysam:

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends pyyaml:

>5.1

depends scikit-learn:

depends scipy:

depends seaborn-base:

>=0.9.1

depends svist4get:

>=1.2.24

depends xgboost:

>=0.71

depends xlsxwriter:

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 tobias

and update with::

   mamba update tobias

To create a new environment, run:

mamba create --name myenvname tobias

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/tobias:<tag>

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

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