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HB_INSTALL.md

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Installing the Genomic HyperBrowser

Software requirements

The following pieces of software must be installed prior to installing the Genomic HyperBrowser:

  • Python 2.7
  • R 3.2 or later
  • Perl 5.8 or later
  • Numpy 1.7.0 or later
  • ImageMagick 6.2.8 or later (only for use in generating Google map-based heatmaps)
  • rsync

Make sure that all software is available for the setup script (e.g. using PATH, PYTHONPATH, RHOME and R_LIBS paths.)

Installation procedure

  1. Make a copy the 'config/galaxy.ini.sample' file, named 'config/galaxy.ini', and edit this according to standard Galaxy configuration:

    • Make sure that the configuration options id_secret and proto_id_secret are set to different non-default values. Otherwise, no HyperBrowser specific options need to be changed from the default values.

    • In order to access your installation from other computers, you need to set the host option to 0.0.0.0

  2. Enter the Galaxy folder and start Galaxy:

    sh run.sh

    Note that will take a long time in the first startup due to compiling of Python and R packages, as well as setting up HyperBrowser test data.

    Watch the output log for any errors.

    To shut down the server, type Ctrl-K

  3. By default, the Genomic HyperBrowser will be available at:

    https://hostname:8080

    Where hostname by default is "localhost"

  4. To run the Genomic HyperBrowser in the background, use:

    sh run.sh --daemon

    to start the server, and:

    sh run.sh --stop-daemon

    to shut it down.

    Watch paster.log for any errors when you start the process as a daemon.

  5. More advanced setup and configuration will in most cases be equal to standard Galaxy setup. Please consult the online documentation at:

    https://galaxyproject.org/admin/get-galaxy/

Contact

If you encounter any problems, feel free to contact us at hyperbrowser-bugs@usit.uio.no. Note that the Genomic HyperBrowser currently does not support updating an existing installation running on an older Galaxy version. If this is important for you, please contact us.