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Malcolm McRoberts

Malcolm McRoberts's Public Library

  • Tell Galaxy to use auth_conf file


    In config/galaxy.ini, uncomment the line auth_config_file = config/auth_conf.xml:

    # XML config file that allows the use of different authentication providers # (e.g. LDAP) instead or in addition to local authentication (.sample is used # if default does not exist). auth_config_file = config/auth_conf.xml


    Configure the auth_conf file


    Copy the config/auth_conf.xml.sample and name it config/auth_conf.xml:

    cp config/auth_conf.xml.sample config/auth_conf.xml

    Then configure it appropriately to your LDAP (the documentation in the sample file should be enough).

  • XMLA is "MDX within SOAP within XML within an HTTP packet". 

  • Leveraging Bootstrap and Angular  

      Saturday, April 13, 2013  

    The driving force behind my current Javascript experiment was a need to modernize the UI for the Pivot Table. Clearly the old good JPivot-like UI doesn't match modern users expectations: context menus, drag & drop items, etc. So, once my Javascript cellset fulfilled basic functionality (drill up/down and add/remove hierarchies) I've started my work to rejuvenate the UI into a more stylish one.

    • Have you tried installing the extension directly though the Google store?

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      Kind regards,
      Posts: 740
      Joined: Mon Jun 23, 2014 8:46 am

      Re: Corporate Non-Administrator Extension Install


      Postby Shiseiji » Mon Aug 04, 2014 7:45 am

      A belated thank you! Worked great. Maybe there is something you can put on the on-line log-on site mentioning the Google Store extension? It was seeing the notice every time I visited the site and, I thought, not being able to do anything about that got frustrating.

  • These are revolutionary components of Galaxy allowing users to do interactive data processing from within Galaxy. IEs are built as standard Galaxy visualization plugins, however they launch Docker containers and use some additional routing information to connect end users through the Galaxy server, to the Docker images.
  • "Enterprise" Deployments


    There are some extra considerations with "enterprise" deployments like running docker on a dedicated machine, and having everything under a single /galaxy URL that users will be accessing your services at

  • IPython Integration
  • The IPython plugin allows users to launch and securely connect to an IPython server running in a Docker container, fetch data from their Galaxy history, use the full-feature IPython runtime environment to analyze it, and finally push results back into their history. A YouTube video of the plugin in action can be found

  • it has been integrated as core feature into Galaxy
  • The only requirement is to have Docker
    • Features

      • run IPython directly in your Galaxy main window or in Galaxy Scratchbook
      • complete encapsulated python environment with matplotlib, pandas and friends installed
      • access to all datasets from your current history via pre-defined IPython function
      • manipulate and plot data as you like and export your new files back into the Galaxy history
      • access your Galaxy instance from IPython with bioblend and redefined functions
      • save the IPython Notebook into your Galaxy history
      • notebook persistence across sessions
      • saved IPython Notebook files can be viewed in HTML and re-opened
      • self-closing and cleaning IPython docker container

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