MarkerMiner is an easy-to-use, fully automated, open-access bioinformatic workflow and web application for effective discovery of SCN loci in flowering plants angiosperms (flowering plants), from user-provided angiosperm transcriptome assemblies (e.g. OneKP transcriptome assemblies). It can be run locally or via the web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development.
View the user manual here.
Please refer to INSTALL for detailed instructions.
- Python (>= 2.7)
- Modules: Please refer to pip requirements.txt for list of required modules
- Apache httpd (http://httpd.apache.org)
- Apache mod_wsgi module (https://code.google.com/p/modwsgi/)
## Clone the repository locally
$ git clone --recursive https://github.com/vivekkrish/markerminer-webapp.git
$ cd markerminer-webapp
## Edit the site.cfg and set the UPLOADS_DIRECTORY
## This directory is used by the webapp to store and process uploaded transcript files
## Install required python dependencies
$ pip install -r requirements.txt
## Run the following command to start MarkerMiner webapp
## This initiates a live reloading service, serving the webapp
## This server also listens for code changes and appropriately auto-reloads the application
## To stop the server, hit Control + C
$ python markerminer.py
* Running on http://0.0.0.0:5000/
* Restarting with reloader
### To deploy webapp in production mode, run the ./setup.sh script