ubu | UNC-Chapel Hill Bioinformatics Utilities | Wiki library

by mozack Java Version: v1.2b License: No License

X-Ray Key Features Code Snippets Community Discussions(9)Vulnerabilities Install Support

kandi X-RAY | ubu Summary

ubu is a Java library typically used in Web Site, Wiki applications. ubu has no bugs, it has no vulnerabilities, it has build file available and it has low support. You can download it from GitHub.

Contact: (Lisle Mose) lmose at unc dot edu. See documentation on the wiki: Please see the wiki for usage. There is no need to build under most circumstances - just use a pre-compiled jar available from the downloads link on the wiki.

Support

Quality

Security

License

Reuse

Support

ubu has a low active ecosystem.

It has 20 star(s) with 15 fork(s). There are 3 watchers for this library.

It had no major release in the last 12 months.

There are 2 open issues and 2 have been closed. On average issues are closed in 315 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of ubu is v1.2b

Quality

ubu has 0 bugs and 0 code smells.

Security

ubu has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

ubu code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

ubu does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

ubu releases are available to install and integrate.

Build file is available. You can build the component from source.

It has 5229 lines of code, 504 functions and 63 files.

It has medium code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed ubu and discovered the below as its top functions. This is intended to give you an instant insight into ubu implemented functionality, and help decide if they suit your requirements.

Main function for testing
Re - align samer
Combines two chimer sequences
Adjust the reads from the original reads
The main method
Combine two chimer sequences
Combines the specified BAM into the output
Runs a shell command with the specified arguments
Runs a shell command
Validates the input
Command - line aggregation
Gets the next read
Compare to the given range
Merge the Contigs that overlap the given set of contigs
Prints out the CGG code
Validates the configuration
Utility method to get the gene reads from the given arguments
Test program
Main method for testing
Gets the option parser
Parses the splice junction file
Main method for testing
Runs the reAligner
Extract the extracted region from the input region
Converts the Contigs to BAM file format
Entry point to the gene read statistics

Get all kandi verified functions for this library.

ubu Key Features

No Key Features are available at this moment for ubu.

ubu Examples and Code Snippets

No Code Snippets are available at this moment for ubu.

Community Discussions

Trending Discussions on ubu

Docker Volumes on WSL2

502 Error Bad Gateway on EC2 instance (Nginx)

Server Sent Events not being sent on Google App Engine but work fine locally. How to send multiple messages from sever?

Validate rows from a Pandas dataframe are equal between values in columns

git worktree with relative path?

SYS_TIME capability now working in kubernetes

Cannot send UDP message between 2 local computers with node.js

PowerShell error in VBoxManage unregistervm --delete

Command `docker` can not work with pipeline. Do not work with `|`, `>`, `>>`

QUESTION

Docker Volumes on WSL2

Asked 2021-Jul-17 at 18:12

When I try running a container with a volume that I created on WSL2, it fails to start.
Creating the volume and container with the exact same syntax on a full Ubuntu machine works just fine.

What am I doing wrong?

...

ANSWER

Answered 2021-Jul-17 at 18:12

Your --volume/-v syntax doesn't look right. You aren't specifying the path where it should be mounted inside the container.

Try:

Source https://stackoverflow.com/questions/68421984

QUESTION

502 Error Bad Gateway on EC2 instance (Nginx)

Asked 2021-May-26 at 10:34

I created my own AWS EC2 instance yesterday, and it was working all fine and dandy. Today I went to use it again and I received the 502 error.

(I don't know if this is the reason, but I installed some code listed here: https://blog.quantinsti.com/install-ta-lib-python/ twice. Why ? I didn't even need to do it, I'm just an idiot. It stopped working almost immediately after I did this)

This is my error log when i enter the command : sudo tail -30 /var/log/nginx/error.log

...

ANSWER

Answered 2021-May-26 at 09:55

Check if the connection settings to upstream is correct.

Also you can check the memory usage by using:

Source https://stackoverflow.com/questions/67697660

QUESTION

Server Sent Events not being sent on Google App Engine but work fine locally. How to send multiple messages from sever?

Asked 2021-Apr-16 at 17:54

Goal

I need my backend to push several answers to my client and I need puppeteer to run backend-side. Puppeteer needs some time to work, but has regular intermediate results and should send updates to the client regulary (in total, one request-responses-cycle takes less than 60secs which seems to be the upper limit for GAE).

Underlying GAE Problem:

Websockets do not work with the standard environment.
Puppeteer does not work with the flex environment.

Main Problem

As a consequence, I re-implemented my code to use server sent events (which is based on http). I expected that to work in standard. It works fine locally. It does not work on production. It will eventually answer the client but only when I close the connection server side and then send everything in one go. It does not regularly update the client. This only happens on GAE, not locally.

What have I tried?

I do flush the sse-response, as otherwise the compression nodejs library leads to a similar behaviour

I also set these headers, esp. X-Accel-Buffering, taken from here:

...

ANSWER

Answered 2021-Apr-16 at 17:54

Your local GAE [standard] environment is not an exact replica or simulation of GAE production. This is especially true if you are using GAE Python2 standard. You should keep that in mind going forward. I know this because I have also experienced this issue with Server Sent Events. This means something that works in dev environment might not work in production so be very careful to first confirm what works and doesn't in GAE documentation.
GAE standard does not support streaming which is essentially what SSEs are. In addition, App Engine standard has a deadline of 1 minute for each request i.e. each call to App Engine as part of your standard app has to return within a minute
I don't believe GAE Flexible have these restrictions so you should try it. See this link which talks about differences between standard and flexible. When I had this issue years ago (trying to do SSE on Python), I ended up switching to Compute Engine and doing PubSub but there were other reasons for going that route instead of trying GAE Flexible

Source https://stackoverflow.com/questions/67117233

QUESTION

Validate rows from a Pandas dataframe are equal between values in columns

Asked 2021-Apr-01 at 08:04

Say I have a pandas DataFrame as below:

...

ANSWER

Answered 2021-Apr-01 at 07:25

You can use DataFrameGroupBy.nunique and compare for not equal 1 by DataFrame.ne:

Source https://stackoverflow.com/questions/66899838

QUESTION

git worktree with relative path?

Asked 2021-Mar-23 at 11:20

I have a master and a setup branch in my repo. I'm keeping the setup branch checked out as a worktree inside the main repo folder via

...

ANSWER

Answered 2021-Mar-15 at 10:15

You are not the first to ask this question, see this feature-request from 2016

Relative paths seem to complicate things:

when moving a worktree (note that a worktree can be inside or outside the parent repository)
when moving the parent repository

So it seems this never got implemented...

Source https://stackoverflow.com/questions/66635437

QUESTION

SYS_TIME capability now working in kubernetes

Asked 2020-May-05 at 17:20

When I created a pod with below security context having permission to change system time am getting error

...

ANSWER

Answered 2020-May-05 at 17:20

To change system time, you will have to run the container as root:

Source https://stackoverflow.com/questions/61616892

QUESTION

Cannot send UDP message between 2 local computers with node.js

Asked 2020-Apr-18 at 17:51

I have a UDP server on one machine and a client on the another. I am not able to receive a message sent by a client on the server machine over the local network or through the internet. My ultimate goal is to have the server on my internal network and the client on a hosted virtual server in the cloud.

When I run the same server and client on the same machine they talk perfectly. The firewall on the ubuntu server hosting the UDP server is inactive.

...

ANSWER

Answered 2020-Apr-18 at 17:51

Changing the UDP server address to 0.0.0.0 instead of 127.0.0.1 did the trick.

Source https://stackoverflow.com/questions/61293055

QUESTION

PowerShell error in VBoxManage unregistervm --delete

Asked 2020-Mar-24 at 10:03

Why does the try part work fine, but catch part gives an error? Weird thing is that even though it gives an error, it still does the deletion. Any ideas?

...

ANSWER

Answered 2020-Mar-24 at 10:03

As you can see in your error output, PowerShell tries to execute the output of the following line:

Source https://stackoverflow.com/questions/60814409

QUESTION

Command `docker` can not work with pipeline. Do not work with `|`, `>`, `>>`

Asked 2020-Jan-10 at 07:02

I want to search some text output by command docker, but it seems not work with pipeline.

My expected result of docker > a should write all output in the terminal to file a. And expected result of docker | grep info should print something that contains info Display system-wide information.

I added myself to the group docker. The following is test cases.

...

ANSWER

Answered 2020-Jan-10 at 06:54

that is because , docker command need some arguments that is it returing errors, you can use this:

Source https://stackoverflow.com/questions/59676625

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install ubu

You can download it from GitHub.
You can use ubu like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the ubu component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

Find more information at: