Pinery is a web service application that provides generalized LIMS (Laboratory Information Management System) access for information about samples.
The Pinery plugin provides three input formats:
pinery_ius contains lane and sequenced sample information, and excludes
skipped lanes and samplespinery_ius_include_skipped contains lane and sequenced sample information, including
skipped lanes and samplespinery_projects provides the projects informationTo configure a Pinery source, create a JSON file ending in .pinery as follows:
{
"clinicalPipelines": ["Clinical", "Accredited Pipeline"],
"provider": "foo-v2",
"shortProvider": "foo",
"url": "http://pinery:8080/",
"version": 2
}
where provider is an arbitrary string that will be baked into the
provider field for pinery_ius and pinery_ius_include_skipped. shortProvider is
similar, but will be used in external_key. url is the address of the Pinery
server and version provides the Pinery data model version.
For each configuration, the names of all and active projects are also available as constants.
There are functions and constants that separate out clinical projects. If "clinicalPipelines" is
set to an array, then any pipeline listed will be considered clinical. If it is null, then the
legacy behaviour is enabled where the pipeline Clinical or any pipeline starting with Accredited
will be considered clinical.