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:

1.0.6-0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

requirements:

Installation

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 me-pcr

and update with::

   mamba update me-pcr

To create a new environment, run:

mamba create --name myenvname me-pcr

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 quay.io/biocontainers/me-pcr:<tag>

(see `me-pcr/tags`_ for valid values for ``<tag>``)

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