recipe bioconductor-rgmql

GenoMetric Query Language for R/Bioconductor

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/RGMQL.html

License:

Artistic-2.0

Recipe:

/bioconductor-rgmql/meta.yaml

This package brings the GenoMetric Query Language (GMQL) functionalities into the R environment. GMQL is a high-level, declarative language to manage heterogeneous genomic datasets for biomedical purposes, using simple queries to process genomic regions and their metadata and properties. GMQL adopts algorithms efficiently designed for big data using cloud-computing technologies (like Apache Hadoop and Spark) allowing GMQL to run on modern infrastructures, in order to achieve scalability and high performance. It allows to create, manipulate and extract genomic data from different data sources both locally and remotely. Our RGMQL functions allow complex queries and processing leveraging on the R idiomatic paradigm. The RGMQL package also provides a rich set of ancillary classes that allow sophisticated input/output management and sorting, such as: ASC, DESC, BAG, MIN, MAX, SUM, AVG, MEDIAN, STD, Q1, Q2, Q3 (and many others). Note that many RGMQL functions are not directly executed in R environment, but are deferred until real execution is issued.

package bioconductor-rgmql

versions:

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.1-0,  1.10.0-1,  1.10.0-0,  1.6.0-1,  1.4.1-0, 

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.1-0,  1.10.0-1,  1.10.0-0,  1.6.0-1,  1.4.1-0,  1.2.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-rgmqllib:

>=1.22.0,<1.23.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dplyr:

depends r-glue:

depends r-httr:

depends r-plyr:

depends r-rjava:

depends r-xml2:

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-rgmql

and update with::

   mamba update bioconductor-rgmql

To create a new environment, run:

mamba create --name myenvname bioconductor-rgmql

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-rgmql:<tag>

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

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