recipe hicup

A tool for mapping and performing quality control on Hi-C data

Homepage:

http://www.bioinformatics.babraham.ac.uk/projects/hicup/

License:

GPLv3

Recipe:

/hicup/meta.yaml

Links:

biotools: hicup, doi: 10.12688/f1000research.7334.1

package hicup

versions:

0.9.2-1,  0.9.2-0,  0.8.3-1,  0.8.3-0,  0.8.2-0,  0.8.1-0,  0.7.3-1,  0.7.3-0,  0.7.2-0, 

0.9.2-1,  0.9.2-0,  0.8.3-1,  0.8.3-0,  0.8.2-0,  0.8.1-0,  0.7.3-1,  0.7.3-0,  0.7.2-0,  0.6.1-1,  0.6.1-0,  0.5.10-0,  0.5.9-0

depends bowtie:

depends bowtie2:

depends pandoc:

depends perl:

depends perl-bioperl:

depends r-base:

depends r-plotly:

depends r-rmarkdown:

depends r-stringi:

>=1.7.8

depends r-tidyverse:

depends samtools:

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 hicup

and update with::

   mamba update hicup

To create a new environment, run:

mamba create --name myenvname hicup

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/hicup:<tag>

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

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