Install

Download required softwares and databases for running RainBow.

git clone https://github.com/rg-korea/rainbow.git
cd rainbow
bash setup.sh

Activate the installed conda environment

The install file created a conda environment called rainbow. You have to activate this environment before using rainbow.

source activate rainbow

Copy and edit the config .ini file

Edit the config file so that the parameters and directory names fit your analysis needs. The recommended method is that you copy the example.ini file from the example_data folder, and edit the contents, as follows.

cp example_data/example.ini my_config.ini

Note that when editing the data_dir of the config file, you should make sure that all fastq files are in fastq(.gz) format, and the files should end in either _1.fastq.gz, _1.fastq, _2.fastq.gz or _2.fastq.

Run

After getting your own copy of the config file, now you can run the rainbow pipeline.

python rainbow.py -i /path/to/your/my_config.ini

Third party software/database license

RainBow contains files not developed by the Rare Genomics Institute Korea. Files in the subdirectory bin/ and files downloaded by setup.py follow their own licenses. We recommend you read them, since not all of them follow the same license as RainBow.

License

RainBow follows The MIT License (MIT). This license applies to all parts of this software except the third party software/databases documented in THIRD-PARTY-NOTICES.txt. For further information, we recommend you read our LICENSE.txt or the contents in https://opensource.org/licenses/MIT