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Installing and configuring the server

If you want to do more than just displaying static CSV files, you need to configure your server components. Also, see HOWTO: Get the search repos example to work.

Requirements

Make sure you have the following packages installed:

  • PHP 5.3+ with the following extensions:
    • curl
    • pdo_sqlite
    • mbstring
    • fileinfo
  • R 3.3+ (https://www.r-project.org/) with current updates, with the following libraries. Make sure you install these packages for all users, so that Apache can load them.
    • GMD
    • MASS
    • ecodist
    • jsonlite
    • tm (Version 0.6 - do not use 0.7)
    • proxy
    • SnowballC
    • rplos
    • parfossil
    • doParallel
    • rentrez
    • curl
    • tibble
    • data.table
    • stringi
    • stringdist
    • xml2 (Version 1.0 or higher)
    • jaod (Currently, a Github repository only: http://github.com/ropenscilabs/jaod. Install with devtools.)
    • rbace (Currently, a Github repository only: http://github.com/ropenscilabs/rbace. Install with devtools.)
  • phantomjs 2.1+ (http://phantomjs.org/), if you want to use the snapshot feature

Configuration

Set the following variables in php.ini:

  • max_execution_time = 240
  • max_input_time = 480
  • memory_limit = 512M
  • upload_max_filesize = 100M
  • post_max_size = 100M

Duplicate config.ini in server/preprocessing/conf/ and rename it to config_local.ini. Adapt the following variables:

  • general->preprocessing_dir: Full path to the preprocessing directory
  • general->host: Host of the client visualization
  • general->path: Relative path to the client visualization. Needs to be in the public_html/www directory.
  • general->images_path: Full path to the images directory for the client. Needs to be in the public_html/www directory. Make sure that your webserver has write access to this directory.
  • general->services_path: Relative path to the client REST services. Needs to be in the public_html/www directory.
  • calculation->binary: Path to RScript binary
  • connection->sqlite_db: Full path to the sqlite datatabase file. For development purposes, duplicate headstart.sqlite in server/storage/ and rename it to a filename of your choice. Enter the path to this file here. Make sure that your webserver has write access to this file and the containing directory.
  • snapshot->snapshot_enabled: Set to 1 to enable snapshot feature, 0 to disable
  • snapshot->phantomjs_path: Absolute path to phantomjs binary
  • snapshot->getsvg_path: Absolute path to getChartSVG.js
  • snapshot->storage_path: Absolute path to the directory, where the snapshots are stored. Make sure that your webserver has write access to this file and the containing directory.
  • snapshot->snapshot_php: PHP File responsible for rendering the bubble in a way to be snapshotted. Relative path to general->host
  • snapshot->snapshot_width: Thumbnail width