recipe biocamlib

An OCaml foundation upon which a number of the bioinformatics tools are built.






BiOCamLib is an OCaml foundation upon which a number of the bioinformatics tools are built, including KPop <>. It consists of four tools: 1. RC, which can efficiently compute the reverse complement of sequences. 2. Octopus, which is a high-throughput program to compute the transitive closure of strings. 3. Parallel, which allows the splits and processes an input file chunk-wise using a reader/workers/writer model. 4. FASTools, which is a Swiss-knife tool for the manipulation of FASTA/FASTQ files.

package biocamlib

(downloads) docker_biocamlib





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 biocamlib

and update with::

   mamba update biocamlib

To create a new environment, run:

mamba create --name myenvname biocamlib

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 `biocamlib/tags`_ for valid values for ``<tag>``)

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