IsoProt is a fully reproducible one-stop-shop for the analysis of iTRAQ/TMT data.
Read the IsoProt manuscript at JPR (open access)
Installation
The easiest way to install and run IsoProt is by using our docker-launcher tool. For more information on how to install a ProtProtocol image like IsoProt using docker-launcher have a look at this documentation.
The rest of this document only refers to running the IsoProt image without using docker-launcher. All of these steps are otherwise automatically taken care of by docker-launcher.
Manual installation
IsoProt is a Docker image and can also manually be installed using the docker command line tool. As a prerequestite, Docker needs to be installed on the system. For more information, please have a look at our help pages on installing Docker.
Note: The following instructions refer to your operating system’s command line.
Download the image:
# Download version 0.2 of the image
docker pull protprotocols/isoprot:release-0.2
# Download the latest version of the image
docker pull protprotocols/isoprot:latest
Manually run the image
docker run -it -p 8888:8888 protprotocols/isoprot:release-0.2
Note: Replace the release-0.2 portion with the version of the image you downloaded and want to launch.
This will launch the image and make it available to access on http://localhost:8888.
In order to directly access your computer’s folders through the docker image (recommended option) map local directories to the containers /data (for input data) and OUT (for output data) folders:
docker run -it -p 8888:8888 -v /path/to/my/mgf/files:/data/ -v /path/to/my/result/folder:/home/biodocker/OUT protprotocols/isoprot
Note: When running Docker Toolbox (ie. only available version on Windows 7), local paths must be below C:\Users. Additionally, paths need to specified in the following format:
# to map C:\Users\Johannes\Downloads
docker run -it -p 8888:8888 -v /c/users/johannes/downloads:/data/ -v /c/users/johannes/results:/home/biodocker/OUT protprotocols/isoprot
Access the Notebook
If you launched the image as described above, the Jupyter notebook is available at http://localhost:8888. Simply open the link and access the Jupyter server.
You can start with the example use case by clicking on the file Isobaric_Workflow.ipynb