Please cite: https://pubs.acs.org/doi/full/10.1021/acs.jproteome.0c00857
This repository has been archived and is no longer maintained. The code is provided for historical reference and may contain unpatched or unknown vulnerabilities. It should not be used in production systems.
This Docker container runs PSpecteR, a Shiny web application for tandem LC-MS proteomic data quality control and research. The container is built with a rocker shiny image for R 3.6.1 and includes PhantomJS for image exportation and mono for the R's raw file reading package (rawDiag). The app also contains interfaces to run containerized versions of the peptide database search algorithms MS-GF+ (for bottom-up proteomics) and MSPathFinderT (for top-down proteomics).
We suggest downloading the docker images on Docker Hub and following the install directions there.
https://hub.docker.com/repository/docker/emslcomputing/pspecter/general
If you would like to add your own code and rebuild the containers, build each container within the container directory:
docker build -t pspecter:1.0.0 .
docker build -t msgf:1.0 .
docker build -t mspathfindert:1.0 .
Then define the shared folder between the containers and use the docker compose file in the pspecter_container repo:
In macOS: export PSPECTER_DATA:/path/to/folder/with/data or Windows: $env:PSPECTER_DATA = "path/to/folder/with/data"
Use the docker compose file from the pspecter_container directory within the ForLocalRun under DockerCompose files: docker-compose up
You may also run the pspecter_container by itself, but note that MS-GF+ and MSPathFinderT will not run:
cd /path/to/pspecter_container
docker run -v ${PWD}:/data --rm -p 3838:3838 pspecter:1.0.0
A complete user's manual for PSpecteR can be found here: https://htmlpreview.github.io/?https://github.com/EMSL-Computing/PSpecteR/blob/master/pspecter_container/www/PSpecteR_Manual_ver1_0_0.html