Web UI

Start server

Command line tools

trackplot --start-server --host 127.0.0.1 --port 5000 --plots ./plots

AppImage (Linux/WSL x86_64 users only)

Download the trackplot appimage file from our release

# example with version v0.3.2, please using your interested version according to your needs
export VERSION=0.3.2
chmod +x trackplot-${VERSION}-x86_64.AppImage
./trackplot-${VERSION}-x86_64.AppImage --help

# startup webserver
./trackplot-${VERSION}-x86_64.AppImage --start-server --host 127.0.0.1 --port 5000 --plots ./plots

Note: the --plots were required while using appimages

Docker image (Strong recommended)

We also prepared a docker image of web server, uses could access this by following this,

docker pull ygidtu/trackplot

# Deploy the server
docker run --name trackplot \
  --rm -v $PWD/example:/data -v $PWD/plots/:/plots -p 5000:5000 ygidtu/trackplot \
  --start-server \
  --host 0.0.0.0 \
  --data /data \
  --plots /plots

-p: public and private port for the server, default:5000(public):5000(private) - -v, --volume: mount the working directory to docker container, for example, the $PWD/data could replace by the path to your directory contains all necessary data - --user: prevent docker read and write file using root privileges - the rest usage please check Command line usage

Usage

1. Main page

The main page of the server, user could click the button to create the plot.

2. Configuration page

At this page, user could see a progress bar at the first tip indicating the progress of the current job.

And next, user should fill in the region of interest at second tip and click the confirm button for downstream analysis.

Please note that the region must follow the pattern, chromosome_id:start_site-end_site:strand.

At third tip, user could reset all configurations for another analysis. please be careful, this reset button will remove all information of previous plot.

3. Choose annotation

At first, user should click the Refernce option to select the genomic annotation file (GTF). And GTF without sorting or bgzipping are both fine for the tool.

Then user could define the parameter at the second tip, and click the confirm button to save the current information for the next step. For choosing the annotation file, user could paste the absolute path of GTF or choose the file on webpage.