recipe perl-pcap

NGS reference implementations and helper code for the IGCG/TCGA Pan-Cancer Analysis Project

Homepage:

https://github.com/ICGC-TCGA-PanCancer/PCAP-core

License:

GPLv3

Recipe:

/perl-pcap/meta.yaml

package perl-pcap

versions:

3.5.2-2,  3.5.2-1,  3.5.2-0,  1.11.1-2,  1.11.1-1,  1.11.1-0

depends libgcc-ng:

>=10.3.0

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

depends perl-bio-db-hts:

depends perl-bio-samtools:

depends perl-bioperl:

depends perl-encode-locale:

depends perl-gd:

depends perl-ipc-system-simple:

depends perl-lwp-simple:

depends perl-sanger-cgp-vcf:

depends perl-xml-parser:

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 perl-pcap

and update with::

   mamba update perl-pcap

To create a new environment, run:

mamba create --name myenvname perl-pcap

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-pcap:<tag>

(see `perl-pcap/tags`_ for valid values for ``<tag>``)

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