Installation

We strongly recommend using the latest version of our tool, using a conda environment, as this sorts out all the dependency issues.

Conda

RAPID is available as a recipe in the bioconda channel. If bioconda is not in your channel list (You can see it, with the command “conda info”), you can add it

conda config --add channels bioconda
conda config --add channels conda-forge
You can search for rapid using the following command: ::
conda search rapid

An example command to use RAPID as a conda environment :

conda create --name <environment_name> rapid=<version>

This command creates an environment for RAPID. We advise to use conda environment based approach, as this would not disturb your exisiting installations, and use only the compatible versions of dependencies.

You can find the location of environments in the file ~/.conda/environments.txt

If you wish to test the installation, download the testData folder from the git repository RAPID.

Move to the test data folder. Edit the rapid path variable in the runTest.sh script. Depending on your OS, and conda installation directory, it should look soemthing like

rapid=/home/<username>/miniconda2/envs/<environment_name>/bin/ (or) rapid=/Users/<username>/miniconda2/envs/<environment_name>/bin/

First activate the desired conda environment

source activate <environment_name>

Now, simply run

bash runTest.sh

Upon succesful completion, there should be two folders TestRapid created by rapidStats, and TestCompare from rapidNorm in the testData folder. You should also find the outputs described under the Visualization section.

If there are some errors with R modules, Open R by staying in the conda environment, and update the R modules

update.packages(ask = FALSE, checkBuilt = TRUE)

To move out of the environment, type

source deactivate <environment_name>

Manual

RAPID does not require any compilation.

  • You need to download (or clone) the git repository RAPID.
  • Extract the RAPID/bin/ files in your preferred location.
  • Ensure to give execute permissions to all files in RAPID/bin/ and then add the installed location to PATH variable.

RAPID makes use of the following tools, and requires them to be in your PATH.

  • Bedtools2
  • Bowtie2 (version 2.1.0 or higher)
  • R version 3.2 or higher
  • Samtools (version 0.1.19 or higher)
  • R Packages required:
    • DESeq2, gplots and RColorBrewer (if you are using rapidDiff)
    • ggplot2, scales, pandoc, knitr

Simple Test

After installation you can try running RAPID using the provided script runTest.sh in the testData folder. Ensure to set the rapid path variable in the script. Now, simply run

bash runTest.sh

Upon succesful completion, there should be two folders TestRapid created by rapidStats, and TestCompare from rapidNorm in the testData folder. You should also find the basic statistics output described under the Visualization section.