Cyverse support team was contacted yesterday via the chat module regarding the questions in the description. They did not reply so a mail was sent to support@cyverse.org. Meanwhile, in the Cyverse app, bam2tbi, I was able to send file path to the input parameter but the image stopped running. I was not able to discern the nature to the error.

Amanda from Cyverse Support:
"Apps (non-Agave) can be added to collections. These function much like tags by grouping the apps together for easy findability. To create/manage collections go to the 'collections' tab on the left side of the Discovery Environment (the icon looks like a little building)."

There is a Integrated Genome Browser collection managed my Nowlan Freese where the tool can be added

Cyverse Support Team:
The condor stderr and stdout files should be included in the logs folder once the analysis completes (or fails). They will have odd file names like "condor-stdout-0" and "condor-stderr-0" (without the quotes).
If the condor-stderr-0 and condor-stdout-0 files are missing, then there might be something wrong that's causing the job to fail before the tool actually executes. Some common issues we've seen are input files being moved in the data store before the analysis gets a chance to execute or the Docker image repo being incorrect in the tool definition. You may find more info along those lines in the docker-compose related log files in the logs folder.
If you still can't find the problem, I'd recommend sharing the analysis with support by clicking on the analysis status on the Analyses page and following the instructions that pop up.

Cyverse Support Team:
If you share your analysis with 'siuser' (see instructions below) I can have a look at it. If it's something I recognize I will certainly let you know. If it is something specific to your app/tool I may not be much help.

You can share your analysis by opening the Analyses window and clicking on the corresponding Status for your analysis. This will take you through several troubleshooting steps. If the troubleshooting steps do not solve your problem click the button that says "I still need help!". Clicking this button will present a form you'll need to fill out in order to share your analysis with us.

The docker image pushed to docker hub repository needs modifications because the documentation for developing the Cyverse app does not specify how to use an interactive docker image connecting the app UI and run shell scripts within it. The example mentioned in the documentation uses an executable docker image although "interactive" is an option. For now, the image can be modified to specify the .tbi generator script as an "entrypoint" so that the image is executable.

The Cyverse app failed several times although the input file argument is being correctly passed. However, there is no obvious option in Cyverse app development to mount the local directory which is required for the script to run. So the new strategy is that the igb_tbi_creator.sh is given as the ENTRYPOINT of the container and the argument is overridden as shown here .
However, I believe for the Cyverse app to run, the command that Cyverse would use is a simple "docker run <container_name> <input_argument_array>". Therefore overriding the ENTRYPOINT is difficult without fully understanding the internal workings of Cyverse app development. So a combination of ENTRYPOINT and CMD(for the arguments) is used and it works in its simplest form in the local system and needs testing in the Cyverse environment. The goal is to keep the docker run command as simple as possible as it cannot be used to dynamically change things in the way we run the image. Another assumption is that the Cyverse DE Data environment is automatically mounted when the app is run. If not the input folder can be specified.
Additionally, a numpy error was also found in the bamCoverage so that was addressed as well.

[~aloraine] - It may be worth contacting Sriram Srinivasan and seeing if he would be willing to meet up or have a zoom call. He is located in Cary, NC, so he is not far from us.

Software Engineer Lead, Core Software, University of Arizona | sriram@cyverse.org | https://cyverse.org/team
Linkedin profile: https://www.linkedin.com/in/sriramsrinivasan83/

I sent and email to Sriram in Cyverse with an image attachment (added here as well):
"I am part of the BioViz Connect Team from the Genome Visualization Lab in Charlotte. I was trying to deploy an app in Cyverse using the tool bam2tbi and the job keeps failing. I checked the logs for ‘condor_stderr’ file and ‘condor_stdout’ file but it was not there. I made changes to the docker file, assuming what could be the errors and it continued to fail. I was really hoping to get some help with this. Thank you in advance.

Moreover, I was wondering how to add the ‘Argument’ parameter in the Cyverse app if its possible. I have attached an image of an app that the Cyverse team had created for us which illustrates what I mean by the ‘Argument’ parameter

Regards,
Karthik Raveendran"

Any answer Karthik Raveendran?

I have not received a reply for the above.

As per scrum discussion today, closing this ticket as we are not getting a reply from CyVerse support. We will revisit when we have greater need to create new CyVerse apps.

Also, let's be sure to attend any new tutorials at conferences on how to create apps. (comment from Karthik Raveendran)