recipe bioconductor-pasillabamsubset

Subset of BAM files from "Pasilla" experiment

Homepage:

https://bioconductor.org/packages/3.20/data/experiment/html/pasillaBamSubset.html

License:

LGPL

Recipe:

/bioconductor-pasillabamsubset/meta.yaml

Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped.

package bioconductor-pasillabamsubset

(downloads) docker_bioconductor-pasillabamsubset

Versions:
0.48.0-0,  0.44.0-0,  0.40.0-0,  0.38.0-0,  0.35.0-0,  0.32.0-1,  0.32.0-0,  0.30.0-0,  0.28.0-1, 

0.48.0-0,  0.44.0-0,  0.40.0-0,  0.38.0-0,  0.35.0-0,  0.32.0-1,  0.32.0-0,  0.30.0-0,  0.28.0-1,  0.28.0-0,  0.27.0-0,  0.26.0-0,  0.24.0-0,  0.22.0-1,  0.22.0-0,  0.20.0-0

Depends:

  • on bioconductor-data-packages >=20260207

  • on curl

  • on r-base >=4.5,<4.6.0a0

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-pasillabamsubset

to add into an existing workspace instead, run:

pixi add bioconductor-pasillabamsubset

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-pasillabamsubset

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-pasillabamsubset

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-pasillabamsubset:<tag>

(see bioconductor-pasillabamsubset/tags for valid values for <tag>).

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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