recipe bioconductor-cytoml

A GatingML Interface for Cross Platform Cytometry Data Sharing

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/CytoML.html

License:

AGPL-3.0-only

Recipe:

/bioconductor-cytoml/meta.yaml

Uses platform-specific implemenations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms.

package bioconductor-cytoml

versions:

2.12.0-0,  2.10.0-0,  2.6.0-2,  2.6.0-1,  2.6.0-0,  2.4.0-0,  2.2.2-0,  2.2.1-0,  2.2.0-0, 

2.12.0-0,  2.10.0-0,  2.6.0-2,  2.6.0-1,  2.6.0-0,  2.4.0-0,  2.2.2-0,  2.2.1-0,  2.2.0-0,  2.0.0-0,  1.12.0-0,  1.10.0-1,  1.8.1-0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-cytolib:

>=2.12.0,<2.13.0

depends bioconductor-flowcore:

>=2.12.0,<2.13.0

depends bioconductor-flowworkspace:

>=4.12.0,<4.13.0

depends bioconductor-ggcyto:

>=1.28.0,<1.29.0

depends bioconductor-graph:

>=1.78.0,<1.79.0

depends bioconductor-opencyto:

>=2.12.0,<2.13.0

depends bioconductor-rbgl:

>=1.76.0,<1.77.0

depends bioconductor-rgraphviz:

>=2.44.0,<2.45.0

depends bioconductor-rhdf5lib:

>=1.22.0,<1.23.0

depends bioconductor-rprotobuflib:

>=2.12.0,<2.13.0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends libxml2:

>=2.11.4,<2.12.0a0

depends r-base:

>=4.3,<4.4.0a0

depends r-bh:

>=1.62.0-1

depends r-cpp11:

depends r-data.table:

depends r-dplyr:

depends r-jsonlite:

depends r-tibble:

depends r-xml:

depends r-yaml:

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 bioconductor-cytoml

and update with::

   mamba update bioconductor-cytoml

To create a new environment, run:

mamba create --name myenvname bioconductor-cytoml

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/bioconductor-cytoml:<tag>

(see `bioconductor-cytoml/tags`_ for valid values for ``<tag>``)

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