recipe perl-sanger-cgp-battenberg

detect subclonality and copy number in matched NGS data

Homepage:

https://github.com/cancerit/cgpBattenberg

License:

GPLv3

Recipe:

/perl-sanger-cgp-battenberg/meta.yaml

package perl-sanger-cgp-battenberg

versions:

1.4.1-9,  1.4.1-8,  1.4.1-7,  1.4.1-6,  1.4.1-5,  1.4.1-4,  1.4.1-3,  1.4.1-2,  1.4.1-1

depends cancerit-allelecount:

depends impute2:

depends libgcc-ng:

>=12

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

depends perl-file-sharedir:

depends perl-file-sharedir-install:

depends perl-module-build:

0.4234.*

depends perl-pcap:

depends perl-sanger-cgp-allelecount:

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 perl-sanger-cgp-battenberg

and update with::

   mamba update perl-sanger-cgp-battenberg

To create a new environment, run:

mamba create --name myenvname perl-sanger-cgp-battenberg

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/perl-sanger-cgp-battenberg:<tag>

(see `perl-sanger-cgp-battenberg/tags`_ for valid values for ``<tag>``)

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