Customize Data Locations
This tutorial assumes you have completed our Installing Limelight tutorial through step 4.
By default, our installation tutorial will allow Docker to manage where Limelight stores its data. This
includes things like where MySQL stores its data files, where uploaded scans are stored, and working
directories for processing uploaded data. On Linux (including Windows running Ubuntu), these data will
mostly likely be kept under
It is recommended that you let Docker manage the data directories if you can. However, if you would like to customize where the data are stored for Limelight, follow the steps below.
1. Create data directories
You will need to create the following directories for Limelight to store its data.
MySQL data directory. This is the directory used to store the database.
Spectr upload directory. This the directory used for spectra processing.
Spectr storage directory. This the directory used to store spectra.
Limelight upload directory. This is the directory where uploads are temporarily stored.
Blib conversion work directory. This is the directory where .blib conversions are processed.
Blib destination directory. This is the directory where final .blib files will be stored.
If you are using WSL2 on Windows, specifying a Windows filesystem drive (e.g.,
/mnt/d/) for your
data directories is not supported.
For example, if you would like store store all data in the
/data/limelight-data directory, you would type
# make a parent directory for limelight data sudo mkdir -p /data/limelight-data # make the four directories for storing data sudo mkdir /data/limelight-data/mysql sudo mkdir /data/limelight-data/spectr-upload sudo mkdir /data/limelight-data/spectr-storage sudo mkdir /data/limelight-data/limelight-upload sudo mkdir /data/limelight-data/blib-workdir sudo mkdir /data/limelight-data/blib-download
.env with data storage locations
.env configuration file will need to be updated to include the locations of the data directories.
Open this file using your favorite text editor. On Linux (including Docker on Windows), we’ll assume
nano. To edit the file, type:
# ensure you are in correct directory. if you followed tutorial type: cd ~/limelight # edit the file nano .env
Add the following lines to the end of the file. Substitute the actual directories with directories you chose above. This example uses the example directory names:
MYSQL_DATA_DIRECTORY=/data/limelight-data/mysql SPECTR_UPLOAD_DIRECTORY=/data/limelight-data/spectr-upload SPECTR_STORAGE_DIRECTORY=/data/limelight-data/spectr-storage LIMELIGHT_UPLOAD_DIRECTORY=/data/limelight-data/limelight-upload BLIB_WORK_DIR=/data/limelight-data/blib-workdir BLIB_DESTINATION_DIR=/data/limelight-data/blib-download
Control-x to save and exit
3. Starting and Stopping Limelight
The commands below are different than the commands for starting and stopping Limelight on our Installing Limelight tutorial! You must always use these commands if you have customized the data locations.
At this point, starting and stopping Limelight should be straight forward.
To start Limelight:
sudo docker-compose -f docker-compose-custom-data.yml up --detach
To stop Limelight:
sudo docker-compose -f docker-compose-custom-data.yml down
The first time you start Limelight, all of the components will download and the database will initialize. This may take a few minutes, depending on your download speed. Subsequent startups of Limelight will not require these steps and will be faster.
These commands must be typed while you are in the project code directory. If you followed these instructions, you can ensure you are in this directory by typing:
4. Proceed with installation
You should now proceed to step 6 in our tutorial for installing limelight. However, recall that your command for stopping and starting is different than that listed in the tutorial. (See above.)