Difference between revisions of "WebApollo Embed"
From GMOD
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(→Anatomy of a WebApollo clone) |
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+ | <span style="font-size:36pt;color:red"> | ||
+ | Work in progress: come back later | ||
+ | </span> | ||
=Description of setting up WebApollo as an embedded web application= | =Description of setting up WebApollo as an embedded web application= | ||
==Use case== | ==Use case== | ||
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[[File:refseqs.png]] | [[File:refseqs.png]] | ||
[[File:refseqs_in_db.png]] | [[File:refseqs_in_db.png]] | ||
+ | |||
+ | |||
+ | |||
+ | ==Anatomy of a WebApollo clone== | ||
+ | * The clone of the webapp is almost entirely symbolic links, except where otherwise noted. | ||
+ | * We can't just create a symbolic link to the base WebApollo installation because some of the internal components are real files | ||
WebApollo_clone | WebApollo_clone | ||
− | + | |-- META-INF -> symlink | |
− | + | |-- WEB-INF -> symlink | |
− | + | |-- <b><font color=blue>annotations</font></b> | |
− | + | |-- <b><font color=blue>config</font></b> | |
− | + | | |-- blat_config.xml -> symlink | |
− | + | | |-- canned_comments.xml -> symlink | |
− | + | | |-- chado_config.xml -> symlink | |
− | + | | |-- <b><font color=red>config.xml</font></b> | |
− | + | | |-- gff3_config.xml -> symlink | |
− | + | | |-- hibernate.xml -> symlink | |
− | + | | |-- mapping.xml -> symlink | |
− | + | | |-- track_name_comparator.js -> symlink | |
− | + | | `-- translation_tables -> symlink | |
− | + | |-- images -> symlink | |
− | + | |-- index.html -> symlink | |
− | + | |-- jbrowse | |
− | + | | |-- bin -> symlink | |
− | + | | |-- combination_tracks.css -> symlink | |
− | + | | |-- data | |
− | + | | | |-- names -> symlink | |
− | + | | | |-- <b><font color=green>seq -> symlink</font></b> | |
− | + | | | |-- <b><font color=red>trackList.json</font></b> | |
− | + | | | `-- <b><font color=blue>tracks</font></b> | |
− | + | | | `-- <b><font color=green>EG -> symlink</font></b> | |
− | + | | |-- export_dialog.css -> symlink | |
− | + | | |-- faceted_track_selector.css -> symlink | |
− | + | | |-- file_dialog.css -> symlink | |
− | + | | |-- genome.css -> symlink | |
− | + | | |-- icons.css -> symlink | |
− | + | | |-- img -> symlink | |
− | + | | |-- index.html -> symlink | |
− | + | | |-- jbrowse_conf.json -> symlink | |
− | + | | |-- main.css -> symlink | |
− | + | | |-- maker.css -> symlink | |
− | + | | |-- menubar.css -> symlink | |
− | + | | |-- plugins -> symlink | |
− | + | | |-- sample_data -> symlink | |
− | + | | |-- src -> symlink | |
− | + | | `-- track_styles.css -> symlink | |
− | + | |-- js -> symlink | |
− | + | |-- jslib -> symlink | |
− | + | |-- selectTrack.jsp -> symlink | |
− | + | |-- styles -> symlink | |
− | + | |-- <b><font color=red>tmp</font></b> | |
− | + | |-- userPermissions.jsp -> symlink | |
− | + | `-- user_interfaces -> symlink | |
+ | |||
+ | Key: | ||
+ | <b><font color=blue>local directory</font></b> | ||
+ | <b><font color=red>local file</font></b> | ||
+ | <b><font color=green>symbolic link to species-specific sequence or tracks</font></b> | ||
+ | <b>symbolic link to shared WebApollo files</b> |
Latest revision as of 17:48, 8 October 2013
Work in progress: come back later
Contents
Description of setting up WebApollo as an embedded web application
Use case
- Run WebApollo as an integrated component of a web application
- Support multiple species
- Support multiple users with private editing session
- Users can have multiple projects/species
- Jump straight to edit mode without user login
Installation
- Use the regular installation/configuration procedure
- Use exemplar species sequence annotations, we will add multiple species support below
Unsorted odds and ends
The key thing that must be done for multiple species/users/sessions on one server is creating multiple tomcat webapps by cloning the WebApollo Directory tree.
Anatomy of a WebApollo clone
- The clone of the webapp is almost entirely symbolic links, except where otherwise noted.
- We can't just create a symbolic link to the base WebApollo installation because some of the internal components are real files
WebApollo_clone |-- META-INF -> symlink |-- WEB-INF -> symlink |-- annotations |-- config | |-- blat_config.xml -> symlink | |-- canned_comments.xml -> symlink | |-- chado_config.xml -> symlink | |-- config.xml | |-- gff3_config.xml -> symlink | |-- hibernate.xml -> symlink | |-- mapping.xml -> symlink | |-- track_name_comparator.js -> symlink | `-- translation_tables -> symlink |-- images -> symlink |-- index.html -> symlink |-- jbrowse | |-- bin -> symlink | |-- combination_tracks.css -> symlink | |-- data | | |-- names -> symlink | | |-- seq -> symlink | | |-- trackList.json | | `-- tracks | | `-- EG -> symlink | |-- export_dialog.css -> symlink | |-- faceted_track_selector.css -> symlink | |-- file_dialog.css -> symlink | |-- genome.css -> symlink | |-- icons.css -> symlink | |-- img -> symlink | |-- index.html -> symlink | |-- jbrowse_conf.json -> symlink | |-- main.css -> symlink | |-- maker.css -> symlink | |-- menubar.css -> symlink | |-- plugins -> symlink | |-- sample_data -> symlink | |-- src -> symlink | `-- track_styles.css -> symlink |-- js -> symlink |-- jslib -> symlink |-- selectTrack.jsp -> symlink |-- styles -> symlink |-- tmp |-- userPermissions.jsp -> symlink `-- user_interfaces -> symlink
Key:
local directory local file symbolic link to species-specific sequence or tracks symbolic link to shared WebApollo files