Difference between revisions of "Tripal/tool data"
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| + | <noinclude> | ||
| + | |||
| + | This page stores the data that populates the [[Tripal]] wiki page. | ||
| + | |||
| + | </noinclude> | ||
| + | |||
{{ {{{template}}} | {{ {{{template}}} | ||
| name = Tripal | | name = Tripal | ||
| full_name = | | full_name = | ||
| − | | status = | + | | status = mature |
| − | | dev = active | + | | dev = active |
| − | | os = | + | | support = active |
| + | | type = | ||
| + | | platform = linux, os x, unix, win|platform = linux, os x, unix, win|platform = linux, os x, unix, win|platform = linux, os x, unix, win | ||
| + | | platform = web | ||
| logo = TripalLogo.jpg | | logo = TripalLogo.jpg | ||
| − | | home = http://tripal. | + | | home = http://tripal.info/ |
| about = Tripal is a web front end for [[Chado]] databases, based on the [http://www.drupal.org Drupal] content management system. Tripal leverages many of the features of Drupal--ability to search and edit content, detail pages for different types of content, customizable page layouts, and so on--to provide users with an intuitive, flexible interface to a database. | | about = Tripal is a web front end for [[Chado]] databases, based on the [http://www.drupal.org Drupal] content management system. Tripal leverages many of the features of Drupal--ability to search and edit content, detail pages for different types of content, customizable page layouts, and so on--to provide users with an intuitive, flexible interface to a database. | ||
| Line 23: | Line 32: | ||
* Loaders for GFF3 and FASTA format files. | * Loaders for GFF3 and FASTA format files. | ||
* Provides an API to allow for creation of custom extensions by anyone. | * Provides an API to allow for creation of custom extensions by anyone. | ||
| + | |||
| + | What is tripal capable of? Checkout out the [http://tripal.gmod.oicr.on.ca/1.1/ Demo] instance | ||
| screenshot = | | screenshot = | ||
| public_server = | | public_server = | ||
| − | | dl = | + | | dl = |
| − | | dl_url = http://tripal. | + | | dl_url = http://tripal.info/download |
| dl_src = | | dl_src = | ||
| + | | dl_src_url = | ||
| dl_dev = The latest development version of Tripal is available from the Drupal.org git repositories. Currently Tripal is a sandbox project while it goes through the module application process. For more information regarding the Tripal git repository including common git commands, see [http://drupal.org/node/1337878/git-instructions/6.x-1.x Tripal's Drupal.org project page]. | | dl_dev = The latest development version of Tripal is available from the Drupal.org git repositories. Currently Tripal is a sandbox project while it goes through the module application process. For more information regarding the Tripal git repository including common git commands, see [http://drupal.org/node/1337878/git-instructions/6.x-1.x Tripal's Drupal.org project page]. | ||
| Line 37: | Line 49: | ||
| − | | getting_started_preamble = Full documentation on installing, configuring, and using Tripal is available from the [http://tripal. | + | | dl_dev_url = |
| + | | getting_started_preamble = Full documentation on installing, configuring, and using Tripal is available from the [http://tripal.info/documentation Tripal website]. | ||
| req = | | req = | ||
| install = | | install = | ||
| config = | | config = | ||
| − | | doc = | + | | doc = |
| + | === For Developers === | ||
Tripal provides an API to help developers who wish to create new Tripal extension modules. The API provides common functions for interacting with Chado, Tripal, and for constructing or editing custom templates for a custom look-and-feel. For more information, see the following links: | Tripal provides an API to help developers who wish to create new Tripal extension modules. The API provides common functions for interacting with Chado, Tripal, and for constructing or editing custom templates for a custom look-and-feel. For more information, see the following links: | ||
| Line 47: | Line 61: | ||
* [[Tripal Developer's Handbook]] | * [[Tripal Developer's Handbook]] | ||
| − | | papers = * | + | | papers = * Tripal: a construction toolkit for online genome databases. <ref name=PMID:21959868/> |
| presentations = | | presentations = | ||
| − | | tutorials = | + | | tutorials = |
| − | + | ; [[Tripal Tutorial v1.1]] | |
| − | + | : used during the [[2013 GMOD Summer School]] | |
| − | + | ; [[Tripal Tutorial (v1.0)]] | |
| − | + | : used during the [[2012 GMOD Summer School]] | |
| − | + | ; [[Tripal Tutorial (v0.3.1b)]] | |
| − | + | : The full v0.3.1b tutorial | |
| − | | wild_urls = *[http://www.fagaceae.org Fagaceae Genomics Web] | + | ; [[Tripal Tutorial (v0.3.1b VM)]] |
| + | : for use with the Tripal virtual machine | ||
| + | ; [[Tripal Tutorial (pre version 0.3b)]] | ||
| + | : from the 2010 GMOD Spring School | ||
| + | <!-- ; [[Tripal Tutorial]] - for v0.2 | ||
| + | : from the [[2009 GMOD Summer School - Americas]] --> | ||
| + | | wild_urls = | ||
| + | *[http://www.fagaceae.org Fagaceae Genomics Web] | ||
*[http://www.citrusgenomedb.org/ Citrus Genome Database] | *[http://www.citrusgenomedb.org/ Citrus Genome Database] | ||
*[http://knowpulse2.usask.ca/portal Pulse Crop Genomics and Breeding] | *[http://knowpulse2.usask.ca/portal Pulse Crop Genomics and Breeding] | ||
| Line 72: | Line 93: | ||
| dev_status = | | dev_status = | ||
| contact_email = spficklin@gmail.com | | contact_email = spficklin@gmail.com | ||
| − | | | + | | input = GFF3, FASTA, Chado DB |
| + | | output = | ||
| see_also = | | see_also = | ||
| − | |||
| − | |||
| demo_server = | | demo_server = | ||
| + | | survey_link = | ||
| + | |release date=2009 | ||
| + | | extras = | ||
| + | {{GitcComponent}} | ||
}} | }} | ||
| + | [[Category:Tool data]] | ||
| + | [[Category:GMOD Components]] | ||
| + | [[Category:Tripal]] | ||
[[Category:Tool data]] | [[Category:Tool data]] | ||
[[Category:GMOD Components]] | [[Category:GMOD Components]] | ||
[[Category:Tripal]] | [[Category:Tripal]] | ||
Latest revision as of 18:39, 10 September 2013
This page stores the data that populates the Tripal wiki page.
{{ {{{template}}} | name = Tripal | full_name = | status = mature | dev = active | support = active | type = | platform = linux, os x, unix, win|platform = linux, os x, unix, win|platform = linux, os x, unix, win|platform = linux, os x, unix, win | platform = web | logo = TripalLogo.jpg | home = http://tripal.info/ | about = Tripal is a web front end for Chado databases, based on the Drupal content management system. Tripal leverages many of the features of Drupal--ability to search and edit content, detail pages for different types of content, customizable page layouts, and so on--to provide users with an intuitive, flexible interface to a database.
Features and advantages of Tripal:
- Allows rapid development of an online genomic database.
- Site administrators can add non-biological content to their sites and allow editing of content by non-technical users.
- Integrates directly with GMOD Chado.
- Provides visualizations for Chado "modules" such as features, analyses, libraries, stocks, and others.
- Provides an interface for easy editing/updating of data in Chado.
- Provides full text and categorical search capabilities for Chado content.
- Can integrate GMOD tools such as CMap and GBrowse.
- Integrates with powerful Drupal features like Drupal views and panels
- Provides fully customizable PHP-based templates to allow users to change the look and feel of their installation
- Web-based management of Chado (i.e. installation of Chado v1.11 and loading of ontologies)
- Loaders for GFF3 and FASTA format files.
- Provides an API to allow for creation of custom extensions by anyone.
What is tripal capable of? Checkout out the Demo instance | screenshot = | public_server = | dl = | dl_url = http://tripal.info/download | dl_src = | dl_src_url = | dl_dev = The latest development version of Tripal is available from the Drupal.org git repositories. Currently Tripal is a sandbox project while it goes through the module application process. For more information regarding the Tripal git repository including common git commands, see Tripal's Drupal.org project page.
To clone the Tripal development GIT repository, use the following command:
git clone --recursive --branch 6.x-1.x http://git.drupal.org/sandbox/spficklin/1337878.git tripal
You can also browse the Tripal GIT repository.
| dl_dev_url =
| getting_started_preamble = Full documentation on installing, configuring, and using Tripal is available from the Tripal website.
| req =
| install =
| config =
| doc =
For Developers
Tripal provides an API to help developers who wish to create new Tripal extension modules. The API provides common functions for interacting with Chado, Tripal, and for constructing or editing custom templates for a custom look-and-feel. For more information, see the following links:
| papers = * Tripal: a construction toolkit for online genome databases. [1]
| presentations = | tutorials =
- Tripal Tutorial v1.1
- used during the 2013 GMOD Summer School
- Tripal Tutorial (v1.0)
- used during the 2012 GMOD Summer School
- Tripal Tutorial (v0.3.1b)
- The full v0.3.1b tutorial
- Tripal Tutorial (v0.3.1b VM)
- for use with the Tripal virtual machine
- Tripal Tutorial (pre version 0.3b)
- from the 2010 GMOD Spring School
| wild_urls =
- Fagaceae Genomics Web
- Citrus Genome Database
- Pulse Crop Genomics and Breeding
- Marine Genomics Project (MG.org)
- Cacao Genome Database
- Genome Database for Vaccinium
- Cool Season Food Legume Genome Database
- Genome Database for Rosaceae
- Hardwood Genomics Project
| mail =
| Mailing List Link | Description | Archive(s) | |
|---|---|---|---|
| Tripal | gmod-tripal | Tripal-related announcements, questions, and requests for help from developers and the community. | Nabble (2010/05+), Sourceforge |
| gmod-tripal-devel | Tripal development list | Nabble, Sourceforge |
| logo_info = | dev_ppl = Tripal is under development at several institutions, including the Mainlab Bioinformatics at Washington Statue University, the University of Saskatchewan and the Clemson University Genomics Institute (CUGI). | dev_status = | contact_email = spficklin@gmail.com | input = GFF3, FASTA, Chado DB | output = | see_also = | demo_server = | survey_link = |release date=2009 | extras =
Included in
}}
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