Filter for generating image thumbnails and extracting metadata from FCS files for MyTardis using Bioconductor's flowCore and flowViz packages.

• R (http://www-r-project.org/)
• flowCore (http://www.bioconductor.org/packages/release/bioc/html/flowCore.html)
• flowViz (http://www.bioconductor.org/packages/release/bioc/html/flowViz.html)
• rpy2 (http://rpy.sourceforge.net/)
  • Future versions may use littler (http://dirk.eddelbuettel.com/code/littler.html) instead.
• ImageMagick (http://www.imagemagick.org/script/command-line-tools.php)

• Install ImageMagick, using sudo apt-get install imagemagick

Git clone this repository into /path/to/mytardis/tardis/tardis_portal/filters:

git clone git@github.com:wettenhj/fcs-mytardis-filter.git fcs

Add the following to your MyTardis settings file eg. /path/to/mytardis/tardis/settings.py

MIDDLEWARE_CLASSES = MIDDLEWARE_CLASSES + ('tardis.tardis_portal.filters.FilterInitMiddleware',)

FILTER_MIDDLEWARE = (("tardis.tardis_portal.filters", "FilterInitMiddleware"),)

The above enables the filter middleware for all actions.

Then add the definition for this filter.

POST_SAVE_FILTERS = [
   ("tardis.tardis_portal.filters.fcs.fcs.make_filter",
   ["FCS", "http://tardis.edu.au/schemas/fcs/1",
    "/path/to/mytardis/tardis/tardis_portal/filters/fcs/bin/fcsplot",
    "/path/to/mytardis/tardis/tardis_portal/filters/fcs/bin/showinf"])
   ]

cd /path/to/mytardis and load the parameter schema into the MyTardis database:

python mytardis.py loaddata tardis/tardis_portal/filters/fcs/fcs.json

Restart MyTardis.