recipe gimmemotifs

Motif prediction pipeline and various motif-related tools

Homepage:

https://github.com/vanheeringen-lab/gimmemotifs

License:

MIT

Recipe:

/gimmemotifs/meta.yaml

Links:

biotools: gimmemotifs

Motif prediction pipeline and various motif-related tools

package gimmemotifs

(downloads) docker_gimmemotifs

versions:
0.18.0-50.18.0-40.18.0-20.18.0-10.18.0-00.17.2-10.17.2-00.17.1-20.17.1-1

0.18.0-50.18.0-40.18.0-20.18.0-10.18.0-00.17.2-10.17.2-00.17.1-20.17.1-10.17.1-00.17.0-20.17.0-10.17.0-00.16.1-10.16.1-00.16.0-20.16.0-00.15.3-00.15.2-00.15.1-00.15.0-10.15.0-00.14.4-20.14.4-10.14.4-00.14.3-10.14.3-00.14.2-00.14.1-20.14.1-10.14.1-00.14.0-10.14.0-00.13.1-40.13.1-30.13.1-20.13.1-10.13.1-00.13.0-10.13.0-00.12.0-10.12.0-00.11.1-10.11.1-00.10.0-00.10.0b6-10.10.0b5-10.10.0b4-10.10.0b4-00.10.0b1-00.9.0.6-00.9.0.5-00.9.0.4-00.9.0.3-20.8.9.1-1

depends dinamo:

>=1.0

depends gadem:

>=1.3.1

depends gimmemotifs-minimal:

0.18.0.*

depends homer:

>=4.11

depends meme:

>=5.4.1

depends prosampler:

>=1.0

depends trawler:

>=2.0

depends weeder:

>=2.0

depends xxmotif:

>=1.6

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 gimmemotifs

and update with::

   mamba update gimmemotifs

To create a new environment, run:

mamba create --name myenvname gimmemotifs

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/gimmemotifs:<tag>

(see `gimmemotifs/tags`_ for valid values for ``<tag>``)
package gimmemotifs-minimal

(downloads) docker_gimmemotifs-minimal

versions:

0.18.0-50.18.0-40.18.0-20.18.0-10.18.0-00.17.2-10.17.2-00.17.1-2

depends biofluff:

>=3.0.4

depends configparser:

depends diskcache:

depends feather-format:

depends genomepy:

>=0.13.0

depends iteround:

depends jinja2:

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends logomaker:

depends loguru:

depends matplotlib-base:

>=3.3

depends numpy:

>=1.18

depends pandas:

>=1.3,<2

depends pybedtools:

>=0.9.0

depends pysam:

>=0.16

depends python:

>=3.10,<3.11.0a0

depends python-xxhash:

depends python_abi:

3.10.* *_cp310

depends qnorm:

>=0.8.1

depends scikit-learn:

>=0.23.2

depends scipy:

>=1.5

depends seaborn:

>=0.10.1

depends statsmodels:

depends tqdm:

>=4.46.1

depends xdg:

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 gimmemotifs-minimal

and update with::

   mamba update gimmemotifs-minimal

To create a new environment, run:

mamba create --name myenvname gimmemotifs-minimal

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/gimmemotifs-minimal:<tag>

(see `gimmemotifs-minimal/tags`_ for valid values for ``<tag>``)

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