- recipe pal_finder
Find microsatellite repeat elements from sequencing reads and design PCR primers to amplify them
- Homepage:
- License:
GPLv3
- Recipe:
Finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads, and designs PCR primers to amplify these repeat loci in an automated fashion. Exact matches to repeats or 2-, 3-, 4-, 5-, and/or 6-mers are located and primer3 is then used to generate primer pairs to amplify regions containing microsatellite loci.
- package pal_finder¶
- Versions:
0.02.04-4,0.02.04-3,0.02.04-2,0.02.04-1- Depends:
on perl
on primer3
2.0.0a
- 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 pal_finder
to add into an existing workspace instead, run:
pixi add pal_finder
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 pal_finder
Alternatively, to install into a new environment, run:
conda create -n envname pal_finder
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/pal_finder:<tag>
(see pal_finder/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/pal_finder/README.html)
