recipe bioconductor-alabaster.files

Wrappers to Save Common File Formats






Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.

package bioconductor-alabaster.files

(downloads) docker_bioconductor-alabaster.files



depends bioconductor-alabaster.base:


depends bioconductor-biocgenerics:


depends bioconductor-biostrings:


depends bioconductor-rsamtools:


depends bioconductor-rtracklayer:


depends bioconductor-s4vectors:


depends r-base:




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-alabaster.files

and update with::

   mamba update bioconductor-alabaster.files

To create a new environment, run:

mamba create --name myenvname bioconductor-alabaster.files

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<tag>

(see `bioconductor-alabaster.files/tags`_ for valid values for ``<tag>``)

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