recipe cosap

COSAP - Comparative Sequencing Analysis Platform

Homepage:

https://github.com/MBaysanLab/cosap

Documentation:

https://docs.cosap.bio

License:

MIT

Recipe:

/cosap/meta.yaml

package cosap

versions:

0.1.0-0

depends bbmap:

39.01

depends bcftools:

>=1.16,<1.17

depends black:

depends bowtie2:

2.5.1

depends bwa:

0.7.17

depends bwa-mem2:

2.2.1

depends click:

depends docker-py:

depends elprep:

5.1.3

depends fastp:

0.23.2

depends fastqc:

0.11.9

depends gatk4:

>=4.5,<4.6

depends genefuse:

depends libtiff:

depends matplotlib-venn:

depends msisensor-pro:

depends numpy:

depends openjdk:

>=17,<18

depends perl-dbi:

depends perl-lwp-simple:

depends picard:

>=2,<3

depends pillow:

depends pygraphviz:

depends pyranges:

depends python:

>=3.9

depends qualimap:

2.2.2d

depends samtools:

>=1.16,<1.17

depends scikit-learn:

depends seaborn:

depends shortuuid:

depends snakefmt:

depends snakemake:

>=7,<8

depends snpeff:

5.1

depends somatic-sniper:

1.0.5.0

depends upsetplot:

depends vardict-java:

1.8.3

depends varscan:

2.4.4

depends yaml:

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 cosap

and update with::

   mamba update cosap

To create a new environment, run:

mamba create --name myenvname cosap

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/cosap:<tag>

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

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