sgbc / galaksio Goto Github PK

To make it even better I think the right box (History name) should follow the window when scrolling down (and have a bar inside the box to scroll down if the history itself is long).

The outputs list is not clearly multiple choice. It works well if you know that hold control and select all options you want is default but could be made clear with check boxes like in Galaxy.

When selecting between modes (for example Choose computation mode in BamSummary) Galaksio displays a list of check boxes and then the fields dependent on your choice in the check boxes. In Galaxy you instead have a drop down menu of modes which puts the dependent fields in a more clear context (in Galaksio it looks like they are choices for the last option in the checkbox list).

I ran a demo an hour ago and the Galaksio workflow is available in the header but it seems unable to recover the steps.

”New history ” button in History list view is positioned in an odd way compared to the refresh button. .

Subworkflows can be added like tools in Galaxy but the way they are handled in Galaxy mean that they cannot be edited at runtime. For Galaksio this mean that they step throws an error when we try to open it. The error should be replaced with a warning message that things cannot be changed.

See: galaxyproject/galaxy#1887 and galaxyproject/galaxy#4521 for updates in Galaxy.

History available at: https://usegalaxy.org/u/tomkl/h/chip-seq-megakaryocytes
Workflow: https://usegalaxy.org/u/tomkl/w/galaksiocase
Subworkflow (import it and it should be activated by the above workflow): https://usegalaxy.org/u/tomkl/w/subworkflowgalaksiocase
When opening a step with MACS2 callpeak I get an error ”Error while creating the form: Unknown input type section”.

Nodes with more than 2 connections does not have the additional connections being shown.

About workflows takes too much place at the front page. Perhaps make it expandable and have it compressed after first log in?

Dear @fikipollo

Testing more deeply Galaksio, I just find that, if I have quite a lot of histories, I can't select bottom / old history on the second workflow invocation step "history selection". When I try to go down on the page, I can't (it seems this is stopping at the bottom of the content history so datasets at the right of the page). This appears in Firefox as Chrome...

When the workflow fails. Underneath the ”Ooops! Something went wrong during the execution of the workflow” there is a lets take a look to the results” that sends you back to the home page. Some kind of reporting/debugging and the option to retry/save input parameters would be good.

A good way to test this is to trigger workflow failure is to alter the "Effective genome size" in Galaksio with the provided workflows. It is a conditional parameter and kills the workflow..

History available at: https://usegalaxy.org/u/tomkl/h/chip-seq-megakaryocytes
Workflow: https://usegalaxy.org/u/tomkl/w/galaksiocase
Subworkflow (import it and it should be activated by the above workflow): https://usegalaxy.org/u/tomkl/w/subworkflowgalaksiocase

Mino graphics annoyance as it is confusing if the workflows continues to try to load the parameters of the tool or if it is just the animation that keeps going.

The “success” message when sending the workflow is a bit big and makes it look like the workflows i finished.

Sometimes, select inputs does not set the "value" field to all options.
Selecting that option is detected as an error in the form.
Example of tool: Cut (field "Delimited by")

When a workflow fails all input data should be stored so you can solve the problem and run the workflow quickly.

As soon as you close the Galaksio window the workflows becomes forgotten and impossible to retrieve (Workflow invocations menu remains empty).

The Yes/no format used by Galaxy is more clear than checkboxes for input parameters choices.

The red square around empty fields is only visible if the tool is opened. Instead of blanking out the next step button I think it would be appropriate to provide a field listing the steps and specific fields that needs to be filled in before progressing.

There is a recurring error saying that workflow invocations does. This is not only show on the home page view but it pops up when setting up a workflow as well.

When selecting input data it would be good if the label of the first step is displayed. Because right now we have two identically named ”Input dataset collection” in the Galaksio workflow and it is not possible to differentiate them while they in Galaxy they are named 1: Control Fastq List and 2: Treatment Fastq List.

History available at: https://usegalaxy.org/u/tomkl/h/chip-seq-megakaryocytes
Workflow: https://usegalaxy.org/u/tomkl/w/galaksiocase
Subworkflow (import it and it should be activated by the above workflow): https://usegalaxy.org/u/tomkl/w/subworkflowgalaksiocase

The import files from URL function in Galaxy is not mirrored in Galaksio.

See attached image, the view itself does however look more helpful. The "loading steps in workflow" is also running without results as far as I can see.

If I open the a step with the value ”Region of the genome to limit the operation to” then I am forced to fill it in (despite not being a requirement in Galaxy). I can however run the workflow as long as I do not open any step with such an option.

Data to test.
History available at: https://usegalaxy.org/u/tomkl/h/chip-seq-megakaryocytes
Workflow: https://usegalaxy.org/u/tomkl/w/galaksiocase
Subworkflow (import it and it should be activated by the above workflow): https://usegalaxy.org/u/tomkl/w/subworkflowgalaksiocase

https://github.com/fikipollo/galaksio/archive/latest.zip is broken.

After a workflow fails it provides a button with "lets look at the results” but clicking it send you back to Home. Being able to save the input parameters and report an error would be more appropriate.

During test on localhost, I have a cookie issue on firefox
after login, the user name appeared (login ok)
on the right but but view did not changed (sign in page)
I needed to clear localhost cookies to be able to see other pages

When I tried to create a new account, a message "Your account has been created" is shown but I did not receive any email and cannot log in with that account. Login works if you create an account directly in Galaxy but not in Galaksio local server [Create an Account button].

Galaksio treats conditional parameters like if they are editable when they in reality are not (see:
galaxyproject/galaxy#4520 and https://docs.galaxyproject.org/en/master/dev/schema.html#tool-inputs-conditional) If edited in Galaksio and sent to a workflow they will cause a crash. So we need to change how Galaksio treat those fields.

Background posted in link 1
We have a workflow using the MACS2 callpeak tool at Usegalaxy.org. When running the workflow it is impossible to edit the "Effective genome size" unless the workflow is set to "user defined". If it for example is set to M. musculus, then it is impossible to change for this specific tool.

When retrieving the same workflow by API there is no indication that this field is hardcoded in the workflow and if it is altered then the entire workflow crashes before running on the usegalaxy.org server.

Workflow:
https://usegalaxy.org/u/tomkl/w/subworkflowgalaksiocase
Subworkflow that is required to run it:
https://usegalaxy.org/u/tomkl/w/subworkflowgalaksiocase

History with test data:
https://usegalaxy.org/u/tomkl/h/chip-seq-megakaryocytes

The preview for histories when starting a workflow defaults to displaying datasets whenever you switch history to preview. The graphics on top of the preview box is however toggled to collection instead of dataset.

At ”Input data” you immediately get the message ” Some of the required fields are not valid or are empty. Please check the form and try again!”

Users can publish histories on Galaxy just like Workflows. Being able to import histories from the Histories view would be a great way to leverage the capacity of public Galaxy servers.

When an annotation overflows the card of a workflow the last line of the card should be "Click run workflow to read more" so that the user is informed that there is more text.

Running the Mouse ChIP-seq workflow one of the tools fail due to issues with the tool. This cause Galaksio to identify the Workflow as failed and when clicking "Lets look at the results" I am sent to the Home page on Galaksio rather than the results.

This mean that the results become inaccessible.

Clicking previous step at the ”custom parameters” step when you have an empty field means that you cannot move forward from ”Input selection” to fill it in. Moving further back to History selection makes the button clickable but nothing happen and you need to cancel the workflow initiation and redo all steps if you want to run a workflow.

Running two different Galaksio instances on a localhost permits the user to automatically be considered logged in as the wrong users.

This is not a major security hole as the Galaxy server rejects the log in attempt but it is confusing for the user.

Treatment of tools is inconsistent between the GUI layer and the command line.

Certain tool wrappers define a default parameter which on the command line is sent as "no value" (ie no flag at all) still requires a choice to be made on the GUI level. This is problematic when managing tools through the API. Currently Galaksio checks if a required field is empty when importing the workflow JSON from Galaxy and then interprets the required field as optional (in the Galaksio GUI this mean that the default "no value" is pre-selected but any value is accepted).

This does however not work if a Galaxy workflow has been made with a non-default value in a tool which got a required field and where the default value is sent as "no value". Because in such cases the default value is still interpreted as not filling in a required field.

Galaksio is dependent on the user being able to log into an external Galaxy server and does not store any user data locally. Administrator access is based on a list of e-mail addresses and if a user is able to log in to the Galaxy server using an e-mail address on the Galaxy server, then the user is granted access to the administration menu. If the initial set up is botched this mean that it is necessary to delete the Galaksio instance and create a new one, likewise a user is completely blocked from Galaksio when a Galaxy server breaks down or changes IP.

When looking at a workflow you scroll down and then get stuck on the workflow diagram.

Text of each step overlaps each other in workflow diagram

When logging in I get a "Failed while retrieving workflows list" warning in a pop up but all workflows are displayed properly and using the refresh workflow list does not yield a pop up warning.

Clicking the report error button does not seem to do anything.

Name of conditional values should be retrieved in Galaksio from the workflow.

Example: Step 4 in MiModD - Identify a phenotypic mutation in A. thaliana becomes very frustrating as you do not know the name of the Genome version.

https://usegalaxy.eu/u/tomas/w/imported-mimodd---identify-a-phenotypic-mutation-in-a-thaliana

When changing modes (for example Choose computation mode in BamSummary) that cause dependent fields to change. Then Galaksio throws a pop up with message ”Error while creating the form: Unknown value for data type ”null””. I do however not see any issues after receiving the error and can proceed with my workflow.

After importing a history using Galaxy I was unable to use the collections in it as input parameters in my workflow. The collections showed up correctly in the history view but when selecting input they were unavailable in the dropdown menu. They were available when selecting "browse collections" but "use selected" did not allow me to select them as input datasets. After cancelling the workflow and trying again they were available in the dropdown menus.