sanojpunchihewa / f5n Goto Github PK

Describe the bug
When a particular tool or the pipeline is run for a bit large dataset (a few thousand reads), sometimes the log output is not displayed at all. However, it seems to run to the end as the successful message appears after a while in around 30 seconds.

To Reproduce
Steps to reproduce the behavior:

1. launch the f5n app
2. goto standalone and select minimap
3. fill in the arguments and then run the tool
4. Observe that no log output

Expected behavior
The log should be displayed for all runs.

Screenshots

Smartphone (please complete the following information):

• Device: Device: LG Q6
• OS: Android 8.1.0

Use the WrapperObject's methods getPrefix() and getPathToDataDir() to dynamically get the download url of the zip files.

once pipeline stops, go to start page does not check if log is written or not

Is your feature request related to a problem? Please describe.
When job completed, randomly client does not send the processed job result after the ACK from server.

Describe the solution you'd like
To identify the exact bug, add a log dump for MinItAcativity.

Problem-
app crashes in Samsung GT19500 if max memory (default 768M) is not reduced

Solution
Check device memory capacity and set it accordingly (in above case memory should be set to 300M <= Memory <=500M)

Alternative
Inform user about possible failure and let user set the value

At the moment the app only sends a status message to the f5n server

Need to implement the following,

• Upload the newly created files from minimap2, samtools and f5c
• Send the log of the commands

The current version only has permission to write to device storage

• with commands and output

In minIt, after processing if chose to not write the results to a log, btn send results back direct minIt to connect to server state, where it supposed to go to the send result back state.

this I think we have to discuss. user would prefer to run the pipeline on the background.

show args descriptions

It depends on your user base and target audience. While x86 support is needed to run on Chromebooks, how many of your users are actually using your app on them? IIRC, Intel has pretty much given up on x86 chips for mobile devices, so unless you have tons of users on Chromebooks, you can skip it for now.

I think it is not difficult. let's try.

Some of the tools don't display their default values in the configuration UI. To fix this update the JSON files

Describe the bug
While a command is running, if I switch to another app (eg: messenger) and later come back to f5n, the log outputs of f5n are missing (see screenshot). Then if I go back, the app crashes (see screenshot)

To Reproduce
Steps to reproduce the behavior:

1. Run minimap2 on a dataset which takes around 1 minute to run. I tried a small dataset on chr22.
2. While the command is running, goto messenger or any other app
3. After around 2 minutes come back to f5c
4. See that log output is missing
5. then try to go back a few times (the back button in Android)
6. f5n crashes

Screenshots

command run:

after going to another app and coming back things are missing:

Press back button few times:

Smartphone (please complete the following information):

• Device: LG Q6
• OS: Android 8.1.0

Describe the bug
where - commit 61b693f
issue - samsort fails.
error_message - failed to read header from "path/minimap2-out.sam"
possibly because minimap2 erroneously writes the header.

To Reproduce
Steps to reproduce the behavior:

1. run minimap2
2. use minimap2's output for samsort input

Expected behavior
should run samsort

Screenshots

Smartphone (please complete the following information):

• Device: Samsung GT19500
• OS: [Android 5.0.1] armeabi-v7a
• App Version 61b693f

activity name on top of the window would help keep track where you are

the log is shown only when a single pipeline component is run. one way is to have separate text boxes for the number of components.

we can do this in finally block instead of changing f5c,minimap2,samtools src code

init_f5c,init_samtools,init_minimap2 functions all have same code except for the native function.

Describe the bug
When the event align module is run, the output generated is the "f5c_event_align.summary.txt" file instead of the actual alignment output.

To Reproduce
Steps to reproduce the behaviour:
Run f5c event alignment and compare the generated output to that of f5c when run on a computer.

Expected behaviour
The actual event alignment output is expected.

Smartphone (please complete the following information):

• Device: Device: LG Q6
• OS: OS: Android 8.1.0

If nothing is copied to the clipboard the app crashes when PASTE PATH button is clicked

Describe the bug
In the MinIt mode, app crashes when canceled the compress files popup in the upload results state.

To Reproduce
Steps to reproduce the behavior:

1. Process a job in MinIt
2. Go to upload result state in MinIt
3. Press 'Compress Files' and cancel it.
4. App crashes

Expected behavior
Popup should close without crashing the app

Screenshots

Smartphone (please complete the following information):

• Device: LG X Screen
• OS: Android 6
• App Version:

Additional context

• ArrayIndexOutOfBounds Exception

it is easier if copy/paste functionality is added for the activity where IP address is input.

To be changed

• leave mapq value empty
• change -K value to 256

To be added

• --skip-ultra
• --ultra-thresh

Some of the options in f5c are not used in the mobile version. It's better to remove those

• help
• version
• skip unreadable

Check StepActivity.java#L114

https://github.com/hedzr/android-file-chooser?utm_source=android-arsenal.com&utm_medium=referral&utm_campaign=6982

• Cross compile with Android NDK toolchain(Except HDF5)
• Or use Multi CPU architecture support to cross compile(Including HDF5)

after 1b4cf09
1.f5c writes events.summary file to the executing location. --> input the path as a param
2.f5c writes results to the stdout --> input a file path to write results or pipe stdout and flush to a file

The server sets a Generic value to file path args. These values will start with a special character. The app needs to replace those characters with $test_data_set_directory.

$test_data_set_directory will be configured by the user