- recipe longestrunsubsequence
Implementation of a solver for the Longest Run Subsequence Problem. Given a sequence as input, compute a longest subsequence such that there is at most one run for every character.
- Homepage:
- License:
MIT
- Recipe:
This is an implementation of the longest run subsequence problem, introduced in (Schrinner et al., WABI 2020) https://drops.dagstuhl.de/opus/volltexte/2020/12795/. It describes a string problem, which looks for the longest subsequence of a string such that this sequence contains at most one consecutive run for each character in the underlying alphabet. The code contains two different algorithms (based on Integer Linear Programming and on Dynamic Programming) as described in the publication. The problem appears in the context of homology-based scaffolding of two contig sets, originating from two individuals of the same species.
- package longestrunsubsequence¶
- Versions:
1.0.1-0- Depends:
on python
>=3.5
- 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 longestrunsubsequence
to add into an existing workspace instead, run:
pixi add longestrunsubsequence
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 longestrunsubsequence
Alternatively, to install into a new environment, run:
conda create -n envname longestrunsubsequence
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/longestrunsubsequence:<tag>
(see longestrunsubsequence/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/longestrunsubsequence/README.html)
