Integrated Genome Browser contains REST endpoints external programs can use to control IGB or access information from IGB.
IGB Status Check
What it does: Check if IGB is currently running and return the igb version number if successful.
Example: http://127.0.0.1:7085/igbStatusCheck
Request Method: GET
Parameters: none
Successful Response: var igbVersion=9.1.8
Add Data Source
What it does: Add a quickload URL as a new data source to IGB.
Example: http://127.0.0.1:7085/igbDataSource?quickloadurl=https://bitbucket.org/nfreese/quickload-genome-in-a-bottle/raw/release-v1.0.0&quickloadname=NewDataSourceExample
Request Method: GET
Parameters: quickloadurl=The URL of a quickload | quickloadname=The name of the quickload
Successful Response: OK
Bring IGB To Front
What it does: Bring IGB to the front of the user's screen.
Example: http://127.0.0.1:7085/bringIGBToFront
Request Method: GET
Parameters: none
Successful Response: OK
Get Species Version List
What it does: Return a list of the available species in IGB.
Example: http://127.0.0.1:7085/getSpeciesVersionList
Request Method: GET
Parameters: none
Successful Response: {Tetraodon nigroviridis=[T_nigroviridis_Mar_2007, T_nigroviridis_Feb_2004], SARS-CoV-2 virus=[S_virus_Jan_2020], Takifugu rubripes=[T_rubripes_Oct_2011, T_rubripes_Oct_2004, T_rubripes_Aug_2002], Triticum aestivum=[T_aestivum_Aug_2018]}
App Store Get Info
What it does: Return status of specified IGB app.
Example:
POST /manageApp HTTP/1.1
Host: localhost:7090
Content-Type: application/json
Content-Length: 79
{
"symbolicName": "org.lorainelab.igb.protannot",
"action": "getInfo"
}
Request Method: POST
Parameters: JSON containing symbolicName of the app and action set to getInfo
Successful Response: {"status":"UNINSTALLED","appVersion":"9.1.3","symbolicName":"org.lorainelab.igb.protannot","igbVersion":"9.1.8"}
Note: There are additional functions for installing and updating apps. Additional information can be found in the IGB code base at https://bitbucket.org/lorainelab/integrated-genome-browser/src/master/.
IGB Control
What it does: Control IGB view by specifying genome, location, track colors, and loading data.
Example: http://127.0.0.1:7085/IGBControl?version=H_sapiens_Dec_2013&seqid=chr1&start=77050252&end=77050370&loadresidues=false&server_url=
Request Method: GET
Parameters: See https://wiki.bioviz.org/confluence/display/igbdevelopers/Bookmark+REST+API for a full list of parameters
Successful Response: HTML
Note: This endpoint is used by IGB Bookmarks, BioViz Connect, and the eFP-Seq Browser.
IGB Unibrow
What it does: Control IGB view by specifying genome, location, track colors, and loading data.
Example: http://localhost:7085/UnibrowControl?seqid=chr1&end=20636664&start=20633631&version=A_thaliana_Jun_2009
Request Method: GET
Parameters: See https://wiki.bioviz.org/confluence/display/igbman/Controlling+IGB+using+IGB+Links for a full list of parameters
Successful Response: HTML
Galaxy
What it does: Control IGB view by specifying genome, location, and loading data from usegalaxy.org.
Example: http://localhost:7085/igbGalaxyDataView?version=hg38&loadresidues=false&feature_url_0=https://usegalaxy.org/display_application/bbd44e69cb8906b51151c168d4af953c/igb_bed/View/11460dee51146854/data/Tophat_on_data_14_and_data_13__splice_junctions.bed&sym_name_0=Tophat_on_data_14_and_data_13__splice_junctions&sym_method_0=https://usegalaxy.org/display_application/bbd44e69cb8906b51151c168d4af953c/igb_bed/View/11460dee51146854/data/Tophat_on_data_14_and_data_13__splice_junctions.bed&query_url=https://usegalaxy.org/display_application/bbd44e69cb8906b51151c168d4af953c/igb_bed/View/11460dee51146854/data/Tophat_on_data_14_and_data_13__splice_junctions.bed&server_url=galaxy
Request Method: GET
Parameters: version=Galaxy Genome specifier | loadresidues=Set to false | feature_url_0=URL of the Galaxy data | sym_name_0=Name of file as displayed in IGB | sym_method_0=URL of the Galaxy data | query_url=URL of the Galaxy data | server_url=Set to galaxy
Successful Response: HTML