Released: Ready for Use

Tripal SimpleTest Extension Module

Valentin Guignon's picture
This module enables functional testing on Tripal extension modules through Drupal Simpletest module (Drupal core). Examples of .test file can be found here: * https://github.com/tripal/tripal_dt/blob/master/tripal_dt.test * http://cgit.drupalcode.org/tripal_cvb/tree/tripal_cvb.test?h=7.x-1.x * http://cgit.drupalcode.org/brapi/tree/brapi.test

CV Browser Extension Module

Valentin Guignon's picture
This module can be used to display and browse a hierarchical tree representation of any controlled vocabulary (CV) stored into Chado (cvterm table). The vocabulary to browse must have relationships stored into the cvterm_relationship table where the children term is the subject (subject_id) and the parent term is the object (object_id).

Mainlab Chado Loader (sequence, map, marker, QTL, genotype, phenotype, germplasm) Extension Module

ccheng's picture
MCL (Mainlab Chado Loader) is a module that enables users to upload their biological data to chado database schema. Users are required to transfer their biological data into various types of data template files. MCL, then, uploads these data template files into a chado schema. MCL requires each type of data template to have a corresponding class file. MCL predefines the class files for major data template types such as marker, QTL, germplasm, map, project. The flexibility of Chado schema often allows, however, the same type of biological data to be stored in various ways..

Mainlab Chado Search (sequence, map, marker, QTL, genotype, phenotype, germplasm) Extension Module

ccheng's picture
Mainlab Chado Search is a module that enables advanced search function for biological data stored in a Tripal/Chado database. By default, a set of search interfaces are provided, such as 'Gene Search' for searching genes and/or transcripts, 'Marker Search' for searching genetic markers, and 'Sequence Search' for searching any sequences stored in the Chado feature table.

Mainlab Tripal Data Display (sequence, map, marker, QTL, genotype, phenotype, germplasm) Extension Module

ccheng's picture
Mainlab Tripal Data Display contains a set of Drupal/PHP templates that organize and extend the default display of the biological data hosted on a Tripal-enabled site (i.e. http://tripal.info). Supported data type includes orgainsm, marker, QTL, germplasm (stock), map (featuremap), project, heritable phenotypic marker (MTL), environment (ND geolocation), haplotype block, polymorphism, eimage, generic gene (genes created by parsing Genbank files using the Mainlab 'tripal_genbank_parser' module), feature, and pub. Each of the templates can be turned on/off as desired.

ND Genotypes Extension Module

laceysanderson's picture
This module provides a more specialized interface to genotypic information stored in the Chado Natural Diversity module tables including adding summaries of this information to feature pages and providing a powerful marker by germplasm matrix. The module adds specialized panes to marker and variant features to better display/summarize genotypic data.

Tripal Daemon Extension Module

laceysanderson's picture
This module provides the ability to start a Daemon that executes Tripal Jobs. By default, jobs in Tripal's job queue are executed either manually using Drush or via the UNIX cron. However, at most cron can only execute once every minute. The Daemon allows jobs to execute once they are submitted. This is particularly useful if you are allowing non-Tripal Administrators to submit jobs such as is the case with the BLAST UI module.

Tripal Multi-Chado Extension Module

Valentin Guignon's picture
Supports multiple Chado instances in one Tripal installation. Chado instances must be in the same database in different schemata. By default, Chado instance selection is made on a user basis: the administrator can enter in the system the connection information for several Chado databases and assign to each user a specific Chado connection setting.

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