recipe me-pcr

Multithreaded Electronic PCR (in-silico PCR) based on NCBI e-PCR.

Homepage:

https://web.archive.org/web/20100708193215/http://genome.chop.edu/mePCR/

License:

Public Domain

Recipe:

/me-pcr/meta.yaml

Links:

biotools: me-pcr

Multithreaded Electronic PCR (me-PCR) was developed by Kevin Murphy at Children's Hospital of Philadelphia. It is described in Murphy et al (2004) https://doi.org/10.1093/bioinformatics/btg466 and was originally available from http://genome.chop.edu/mePCR (defunct). It was based on the public domain NCBI tool e-PCR by Gregory D. Schuler, described in Schuler (1997) https://doi.org/10.1101/gr.7.5.541 which was origially availble from ftp://ncbi.nlm.nih.gov/pub/schuler/e-PCR/ (defunct). The final release of me-PCR was v1.0.6 (2008-02-18), and the author wrote that in general NCBI e-PCR should be used instead having been improved greatly over the years. The NCBI retired and withdrew the e-PCR webservice and command line tool on 2017-06-28, suggesting the online-only tool Primer-BLAST instead. However, this is not suitable for offline high throughput usage. See also Jim Kent's isPCR (aslo available in BioConda).

package me-pcr

(downloads) docker_me-pcr

Versions:

1.0.6-1,  1.0.6-0

Depends:

  • on libgcc >=13

  • on libstdcxx >=13

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 me-pcr

to add into an existing workspace instead, run:

pixi add me-pcr

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 me-pcr

Alternatively, to install into a new environment, run:

conda create -n envname me-pcr

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/me-pcr:<tag>

(see me-pcr/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.

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