Nowlan Freese added a comment - 30/Sep/22 11:54 AM - edited I created two new apps that allow the user to select bigwig or bedgraph as the output. However, BioViz Connect seems to be having issues with the new "list" parameter included as part of the apps. When the apps were added to the IGB community and the sync apps database endpoint hit, it caused an error that led to the apps not appearing correctly in BioViz Connect. Unclear if we want to spend the time fixing this issue or if we should just release the apps with the output set as bigwig. UPDATE: I created IGBF-3193 to address the issue with BioViz Connect not working with dropdown menus. I have moved the ticket to the backlog as we have decided to move forward with publishing the bigWig output only versions of the Apps. Follow the steps in the previous comment to complete this ticket.

Nowlan Freese added a comment - 06/Oct/22 3:59 PM App names are identical to the original apps. Test input/output data are in iplant/home/shared/BioViz/example_data Both apps have been published. Apps have been synced to bvctest3.bioviz.org for testing. Previous version of apps that produced bedgraph output have been removed from IGB Community. Final steps for testing: Test the new apps on bvctest3.bioviz.org using various accounts (not nowlanf). Run sync apps database on BioViz Connect production. Test the new apps on BioViz Connect production using various accounts (not nowlanf).

Nowlan Freese added a comment - 06/Oct/22 4:47 PM - edited There seems to be an issue where two jobs are being submitted simultaneously for either scaled or unscaled. I have tested twice, and either scaled or unscaled analyses were duplicated. This requires further investigation. Details of the duplicate analyses. Note that the app_id are the same and the startdate are just slightly different. { "description" : "", "name" : "nowlanUnscaled_1" , "can_share" : true , "username" : "nowlan@iplantcollaborative.org" , "app_id" : "6cd156c4-3dd4-11ed-8d36-008cfa5ae621" , "system_id" : "de" , "app_disabled" : false , "batch" : false , "enddate" : "1665088115037" , "app_version_id" : "6cd1ba9c-3dd4-11ed-8d36-008cfa5ae621" , "status" : "Completed" , "id" : "3fba5bee-45b4-11ed-b5bd-008cfa5ae621" , "startdate" : "1665087598141" , "app_description" : "Make a coverage graph file in bigWig format from a bam sequence alignment file using deepTools bamCoverage version 3.3.0 with options --binSize 1. See deeptools.readthedocs.io. %INPUT%bam" , "notify" : true , "resultfolderid" : "/iplant/home/nowlan/analyses" , "app_name" : "Make coverage graph" }, { "description" : "", "name" : "nowlanUnscaled_1" , "can_share" : true , "username" : "nowlan@iplantcollaborative.org" , "app_id" : "6cd156c4-3dd4-11ed-8d36-008cfa5ae621" , "system_id" : "de" , "app_disabled" : false , "batch" : false , "enddate" : "1665087948568" , "app_version_id" : "6cd1ba9c-3dd4-11ed-8d36-008cfa5ae621" , "status" : "Completed" , "id" : "3fb2e92c-45b4-11ed-8f0c-008cfa5ae621" , "startdate" : "1665087598084" , "app_description" : "Make a coverage graph file in bigWig format from a bam sequence alignment file using deepTools bamCoverage version 3.3.0 with options --binSize 1. See deeptools.readthedocs.io. %INPUT%bam" , "notify" : true , "resultfolderid" : "/iplant/home/nowlan/analyses" , "app_name" : "Make coverage graph" },

Nowlan Freese added a comment - 07/Oct/22 11:51 AM - edited Launching analyses from the DE itself does not appear to create duplicates. This would imply something is behaving incorrectly in BioViz Connect. Tested on BioViz Connect with nowlan account on October 7. Running scaled and unscaled coverage graph analyses on community data did not produce duplicate analyses. Possible this was a momentary glitch.

Nowlan Freese added a comment - 11/Oct/22 12:28 PM Final testing on Mac on connect.bioviz.org I ran four analyses using the nowlanf account: Scaled and unscaled coverage graphs on files in user's home folder. Scaled and unscaled coverage graphs on files in community folder. All four analyses completed successfully and the output were visible in IGB. Text description for each analyses appeared correct. Closing ticket