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1. Setup your computer
RUMP is designed to work on Unix-like operating systems. Typically that means Apple OS X (Mac) and Linux.
You may need to log in to a different computer running some flavour of Unix. Windows users may also consider using a virtualisation system such as VirtualBox to provide a Unix system for testing RUMP.
If you don't already have a GitHub account then go to https://github.com/join to create one.
If using Linux, type "Ctrl+Alt+T"; if using MacOS, following this guideline: https://bit.ly/2St56a1. All commands in this Wiki or README of the repo are commands to be typed in Terminal.
If you are using local machine, Docker should be used as the software container. You should be able to run the following command without reporting error.
$ Docker -v
If you are using high-performance computing, Singularity should be used as the software container. You should be able to run the following command without reporting error.
$ singularity version
In your terminal, type
$ git --version
If you don't have git installed, you can install it from https://git-scm.com/downloads. Advanced users may wish to install git from a package management system.
In your terminal, type
$ curl --version
You will need to have curl installed. It is usually pre-installed on OS X and Linux.
Usage
- Setup your computer
- Installing
- Setup your projects with RUMP using local machine
- Setup your projects with RUMP using HiPerGator
- Setup your projects with RUMP using Amazon Web Service
- Executing time estimation
- Data processing parameters modification
Components
- Data collection/generation
- MODIS data quality control
- Data format conversion
- Data processing
- File format transformation
- Statistical analysis
- Unidentified metabolites search
- Pathway analysis
- Report generation
Developers