openPrimeR is an R package providing methods for designing, evaluating,and comparing primer sets for multiplex polymerase chain reaction (PCR). The package provides a primer design function that generates novel primer setes by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers. Moreover, existing primer sets can be evaluated according to their coverage and their fulfillment of constraints on the PCR-relevant physicochemical properties. For PCR tasks for which multiple possible primer sets exist, openPrimeR can facilitate the selection of the most suitable set by performing comparative analyses. The R package includes a Shiny application that provides a comprehensive and intuitive user interface for the core functionalites of the package.
We provide two distributions for openPrimeR. The R package (including the Shiny app) can be retrieved using this GitHub repository. Additionally, we provide a self-contained Docker image for the Shiny application. The openPrimeR Docker image contains all of the dependencies of the tool, which makes it easily usable on any type of system, independent of the installed operating system, R distribution, etc. We recommend that you use the Docker image if you belong to the following groups of users:
- You do not have any experience with R whatsoever and you do not intend to use the functionalities of the R package.
- You only want to use the openPrimeR frontend in terms of the Shiny app.
- You do not want to invest time in installing the package with all of its dependencies.
In a console, enter
**git clone https://github.com/matdoering/openPrimeR-User && ** git submodule update --init --recursive
To update your local version of the tool to the curreent GitHub version at a later point in time, just run
**git pull origin master && ** git submodule update
in the project's base folder.
In case that you have performed changes to the local files and you would like to revert to the last GitHub version, execute
git checkout -- .
in the project folder in order to discard all local changes.
In a console, enter the project's base folder and execute
./install.sh
If you are using Windows, please execute the batch script
./install.cmd
Please ensure that you have added R into your system's path before using the script. For more information, on changing the path, please refer to the R FAQ.h
The installation command installs all of the package's dependencies, that is, other R packages as well as the third-party tools that are required by openPrimeR. If there are problems during the installation, please consider the console output. For example, if you should get an error such as
there is no package called 'gtable'
this can probably be fixed by running
install.packages('gtable')
in case of CRAN packages such as gtable or. For Bioconductor packages, such as XVector, you can run
biocLite('XVector')
after loading biocLite. After this, you restart the installation script. Once the installation is finished, a browser will open the tool. Again, please note the console output here for the case that there were problems with installing the third-party tools.
If you are using Unix/MacOS, simply execute the bash script
./start.sh
from the project's base folder in a console to start a browser with the app.
If you are using Windows, you can run the batch file
start.cmd
located in the project's base folder.
Our docker image is available at dockerhub. In order to use the docker image, you need to install docker on your system and activate the docker daemon.
If you are using Unix/MacOS, please open a console, enter the project's base directory and run the bash script
./start_docker.sh
This procedure will
- Download the Docker image if it isn't available yet.
- Run the Docker image (see details below).
- Start a web browser for using the app.
After logging in with your docker account, in a console, enter
docker pull mdoering88/openprimer
to retrieve the latest docker image of the tool. Since the image is quite large the download (~4 GB) may take some time, especially if your internet connection is not very fast.
To run the image, enter
docker run -p 3838:3838 --rm mdoering88/openprimer
After this, the tool is available by accessing localhost:3838 in your web browser.
In case you want to have more control of the image you are running or you want to study the output of the tool, you can execute
docker run --rm -p 3838:3838 -v /tmp/logs/:/var/log/shiny-server/ mdoering88/openprimer:latest
With this call, the tool's log file is stored in the /tmp/logs/ folder on your system with a filename starting with shiny-shiny). During the session, you can use
tail -f shiny-shiny-X.txt
to retrieve the current status messages.
Moreover, in the above call to Docker, we have specified a tag, namely :latest, which means that we have started the most recent version of the tool. In case that no tag is provided, the latest available Docker image is used.
openPrimeR is being developed at the Max Planck Institute for Informatics and the University of Cologne.
See the LICENSE file for license rights and limitations (GNU General Public License, Version 2.0).
- R >= version 3.4.0
- OS: Linux, MacOS, Windows
- Third-party software: MAFFT, oligoarrayaux, MELTING, phantomjs, selenium for python, ViennaRNA