wettenhj / bam-mytardis-filter

BAM MyTardis Filter

Filter for storing BAM file metadata for MyTardis using samtools.

Requirements

• samtools

Installation

• Install samtools

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

git clone [e-mail]:wettenhj/bam-mytardis-filter.git bam

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.bamfilter.bamfilter.make_filter",
   ["BAM", "http://tardis.edu.au/schemas/bam/1",
    "/path/to/samtools/samtools"]),
   ]

Where the samtools directory is correct for your installation.

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

bin/django loaddata tardis/tardis_portal/filters/bam/bam.json

Restart MyTardis. From now on, all bam files loaded will have metadata extracted and stored alongside the file itself.