- recipe biocamlib
An OCaml foundation upon which a number of the bioinformatics tools are built.
- Homepage:
- License:
GPL-3.0-only
- Recipe:
BiOCamLib is an OCaml foundation upon which a number of the bioinformatics tools are built, including KPop <https://github.com/PaoloRibeca/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¶
- Versions:
1.0.0-0- 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 biocamlib
to add into an existing workspace instead, run:
pixi add biocamlib
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 biocamlib
Alternatively, to install into a new environment, run:
conda create -n envname biocamlib
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/biocamlib:<tag>
(see biocamlib/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.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/biocamlib/README.html)
