TnSeek

TnSeek in practice

  1. Installation of TnSeek

    1. Prerequisites: installation of Docker

      TnSeek relies on the Docker platform to manage dependencies and streamline installation.
      If Docker is not already available on your system, you will need to download and install it first. Please follow this link for installation instructions.


    2. Download of TnSeek and build the Docker image

      3. Once Docker installed on your local machine, to deploy TnSeek, you have to follow the following two steps:

      1. clone the Git repository of TnSeek at https://gitlab.cristal.univ-lille.fr/bonsai/tnseek with:

        2. git clone https://gitlab.cristal.univ-lille.fr/bonsai/tnseek


      2. build the Docker image of TnSeek with:

        3. docker build --tag tnseek -f Dockerfile


        The --tag option specifies the name of the TnSeek image that will be used when running TnSeek. This command may take several minutes but will only need to be executed once. The image will take around 12GB on your local disk.


      As an alternative of the build of the Docker image, you can also download a prepared image at https://bioinfo.univ-lille.fr/tnseek/tnseek.tar.gz, and the run the following command:

      docker load < tnseek.tar.gz

      This command may also take several minutes. This second method is faster but requires downloading a 4GB archive file. Once the TnSeek Docker image is loaded, you can check that the image tnseek:latest is present on your local machine with the docker images command.

  2. Start the application

    3. When you want to launch TnSeek, you have to type the following command:

    docker run -d --rm -p 3838:3838 -p 8787:8787 --cpus 1 \
    -v /etc/localtime:/etc/localtime:ro \
    -v "/pathto/yourdatafolder/":/home/rstudio/playground/ \
    -e USERID=$UID -e PASSWORD=tnphyto \
    --name tnseek \
    tnseek


    where /pathto/yourdatafolder should be replaced with the path to the directory on your local machine that contains your data. It should be a valid existing path.

    The command option -v "/pathto/yourdatafolder/":/home/rstudio/playground/ tells Docker to map your local data directory to the server directory /home/rstudio/playground/. The part /home/rstudio/playground/ should be left unchanged.

    The meaning of the other options is as follows:

    --cpus 1 : the number of CPUs available for the server. By default it's set to 1. On linux distribution you can determine this number with the command nproc. The equivalent for macOS is: sysctl -n hw.logicalcpu.
    -v /etc/localtime:/etc/localtime:ro : Sync the server's time with the host.
    -e USERID=$UID : Ensure that the files generated during the analysis have the right permissions.
    -e PASSWORD=tnphyto : The password used to connect to rstudio (user : rstudio)

  3. Open the application

    4. When the application is up, you will have access to the TnSeek application by opening your favorite web browser at URL http://localhost:3838/
    You will get access to the two mains parts of TnSeek: