recipe deeptools

A set of user-friendly tools for normalization and visualzation of deep-sequencing data

Homepage:

https://github.com/deeptools/deepTools

Documentation:

https://deeptools.readthedocs.io/en/latest/

License:

MIT / MIT

Recipe:

/deeptools/meta.yaml

Links:

biotools: deeptools, doi: 10.1093/nar/gkw257, usegalaxy-eu: deeptools_plot_heatmap, usegalaxy-eu: deeptools_plot_pca, usegalaxy-eu: deeptools_plot_profile, usegalaxy-eu: deeptools_plot_correlation, usegalaxy-eu: deeptools_plot_coverage, usegalaxy-eu: deeptools_plot_fingerprint, usegalaxy-eu: deeptools_plot_enrichment, usegalaxy-eu: deeptools_bam_compare, usegalaxy-eu: deeptools_bam_pe_fragmentsize, usegalaxy-eu: deeptools_bigwig_compare, usegalaxy-eu: deeptools_correct_gc_bias, usegalaxy-eu: deeptools_multi_bam_summary, usegalaxy-eu: deeptools_compute_matrix, usegalaxy-eu: deeptools_compute_gc_bias, usegalaxy-eu: deeptools_multi_bigwig_summary, usegalaxy-eu: deeptools_compute_matrix_operations, usegalaxy-eu: deeptools_alignmentsieve, usegalaxy-eu: deeptools_estimatereadfiltering, usegalaxy-eu: hicup_deduplicator, usegalaxy-eu: deeptools_bigwig_average

package deeptools

versions:

3.5.5-0,  3.5.4-1,  3.5.3-0,  3.5.2-1,  3.5.2-0,  3.5.1-1,  3.5.1-0,  3.5.0-0,  3.4.3-0, 

3.5.5-0,  3.5.4-1,  3.5.3-0,  3.5.2-1,  3.5.2-0,  3.5.1-1,  3.5.1-0,  3.5.0-0,  3.4.3-0,  3.4.2-0,  3.4.1-0,  3.4.0-0,  3.3.2-1,  3.3.2-0,  3.3.1-0,  3.3.0-0,  3.2.1-0,  3.2.0-0,  3.1.3-1,  3.1.3-0,  3.1.2-0,  3.1.1-0,  3.1.0-0,  3.0.2-0,  3.0.1-1,  3.0.1-0,  3.0.0-0,  2.5.7-0,  2.5.6-0,  2.5.5-0,  2.5.4-0,  2.5.3-0,  2.5.2-0,  2.5.1-0,  2.5.0-0,  2.4.3-0,  2.4.2-0,  2.4.1-1,  2.4.1-0,  2.4.0-0,  2.3.6-2,  2.3.6-1,  2.3.5-2,  2.3.5-1,  2.3.5-0,  2.3.4-0,  2.3.3-0,  2.3.2-0,  2.3.1-0,  2.2.4-0,  2.2.3-0,  2.2.2-0,  2.2.1-0,  2.2.0-0,  2.1.0-0,  2.0.1-0,  2.0.0-0,  1.5.9.1-0,  1.5.8.2-0

depends deeptoolsintervals:

>=0.1.8

depends importlib-metadata:

depends matplotlib-base:

>=3.5.0

depends numpy:

>=1.9.0

depends numpydoc:

>=0.5

depends plotly:

>=4.9

depends py2bit:

>=0.2.0

depends pybigwig:

>=0.2.3

depends pysam:

>=0.14.0

depends python:

>=3.8

depends scipy:

>=0.17.0

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 deeptools

and update with::

   mamba update deeptools

To create a new environment, run:

mamba create --name myenvname deeptools

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/deeptools:<tag>

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

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