walrus | Containerized data analysis pipelines | Genomics library

by fjukstad Go Version: Current License: MIT

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | walrus Summary

walrus is a Go library typically used in Artificial Intelligence, Genomics, Docker applications. walrus has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

walrus is a small tool for executing data analysis pipelines using Docker containers. It is very simple: walrus reads a pipeline description from either a JSON or YAML file and starts Docker containers as described in this file. We have used walrus to develop analysis pipelines for analyzing whome-exome as well as RNA sequencing datasets.

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Quality

Security

License

Reuse

Support

walrus has a low active ecosystem.

It has 12 star(s) with 2 fork(s). There are 2 watchers for this library.

It had no major release in the last 6 months.

There are 7 open issues and 14 have been closed. On average issues are closed in 90 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of walrus is current.

Quality

walrus has no bugs reported.

Security

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

License

walrus is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

walrus releases are not available. You will need to build from source code and install.

Installation instructions, examples and code snippets are available.

Top functions reviewed by kandi - BETA

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

run runs the pipeline .
main is the main entry point for testing .
AddData adds new data to the repository
commit returns the commit ID for the given path .
StartServer starts a server
FindAndReplaceVariables finds all variables in a pipeline
PrintDiff returns the diff of the given path .
startPipelineVisualization starts the pipeline .
fixMountPaths fixes the paths in the stage stage
Profile prints container statistics for a container

Get all kandi verified functions for this library.

walrus Key Features

No Key Features are available at this moment for walrus.

walrus Examples and Code Snippets

No Code Snippets are available at this moment for walrus.

Community Discussions

Trending Discussions on walrus

Recursive remove all keys that have NULL as value

Using a walrus operator in if statement does not work

Why does using the walrus operator on a member variable raise a SyntaxError?

Walrus operator, multiple assignments

Error message when trying to nickname someone using discord.py

Why is tqdm only updating after multiple iterations?

Why does "if not a := say_empty()" raise a SyntaxError?

Does java support inline declaration and assignment in a conditional statement?

UnboundLocalError: local variable referenced before assignment within comprehension

Can the walrus operator be used to avoid multiple function calls within a list comprehension?

QUESTION

Recursive remove all keys that have NULL as value

Asked 2021-Jun-14 at 17:54

I have an array of complex dict that have some value as a string "NULL" and I want to remove, my dict looks like this:

...

ANSWER

Answered 2021-Jun-02 at 14:19

Solution:

Source https://stackoverflow.com/questions/67806380

QUESTION

Using a walrus operator in if statement does not work

Asked 2021-May-14 at 15:40

I have a simple function that should output a prefix based on a pattern or None if it does not match. Trying to do a walrus it does not seem to work. Any idea?

...

ANSWER

Answered 2021-May-12 at 10:44

You're setting m to re.match(f'^.+(\d\d)-(\d\d)-(\d\d\d\d)$', name) is not None, which is a boolean.

You probably mean

Source https://stackoverflow.com/questions/67501932

QUESTION

Why does using the walrus operator on a member variable raise a SyntaxError?

Asked 2021-Apr-26 at 12:35

Why can't I use the walrus operator := to assign to an attribute? It works when assigning to a local variable:

...

ANSWER

Answered 2021-Apr-26 at 02:52

The syntax is illegal, as stated in the PEP 572, where the walrus operator (aka "assignment expression") is defined:

Most importantly, since := is an expression, it can be used in contexts where statements are illegal, including lambda functions and comprehensions.

Conversely, assignment expressions don't support the advanced features found in assignment statements:

Single assignment targets other than a single NAME are not supported:

Source https://stackoverflow.com/questions/67260162

QUESTION

Walrus operator, multiple assignments

Asked 2021-Apr-04 at 04:39

I have the following while loop:

...

ANSWER

Answered 2021-Apr-04 at 04:39

I think the closest thing you can do is something like this:

Source https://stackoverflow.com/questions/66937923

QUESTION

Error message when trying to nickname someone using discord.py

Asked 2021-Apr-02 at 04:37

async def on_message(message):
    content = message.content.lower() # The actual content of the message in lowercase
    pattern = "imagine having a name as dumb as (.{0,32})" # Max length for nicks is 32 characters 

    if (nick := re.findall(pattern, content): # Walrus operator, need python 3.8+
        await message.author.edit(nick=nick[0]) # Editing the actual nick

...

ANSWER

Answered 2021-Apr-02 at 04:37

You are missing a closing paranthesis

Source https://stackoverflow.com/questions/66913502

QUESTION

Why is tqdm only updating after multiple iterations?

Asked 2021-Mar-23 at 21:25

I'm using tqdm twice in my script, and the first time it works fine but the second time it only updates after 14 iterations. It's the same if I remove all other print statements. Any idea what might be going wrong?

Program:

...

ANSWER

Answered 2021-Mar-23 at 21:25

tqdm doesn't, by default, show every single update if the updates happen fast; by default it only updates 10 times per second. You can set the miniters parameter to 1 if you must have the output update on every iteration.

The default is miniters=None, which means it'll dynamically adjust the iteration count based on mininterval, which is set to 0.1 seconds.

You are also using print(), which replaces the bar output. Don't do that, updates will be overwritten and you get very messy output.

The tqdm class has a dedicated tqdm.write() method, use that instead:

Source https://stackoverflow.com/questions/66771037

QUESTION

Why does "if not a := say_empty()" raise a SyntaxError?

Asked 2021-Feb-20 at 08:22

PEP 572 introduces the assignement operator ("walrus operator").

The following code works, and outputs empty

...

ANSWER

Answered 2021-Feb-20 at 08:03

Operator precedence indicates that := has a lower precedence than not. So not a := is read as trying to assign to not a, hence the syntax error.

You can use parentheses to clarify the meaning:

Source https://stackoverflow.com/questions/66289224

QUESTION

Does java support inline declaration and assignment in a conditional statement?

Asked 2021-Feb-05 at 01:39

First way (successful):

...

ANSWER

Answered 2021-Feb-05 at 01:01

No, java does not support inline declaration and assignment in a conditional statement.

Source https://stackoverflow.com/questions/66056081

QUESTION

UnboundLocalError: local variable referenced before assignment within comprehension

Asked 2021-Feb-04 at 14:54

I'm playing around with dict comprehensions, and trying PEP572 (the := operator), in an example like this:

...

ANSWER

Answered 2021-Feb-04 at 13:47

You are misusing the condition. It is evaluated once per value retrieved from the iterator; it cannot be used to define the iterator. names isn't yet defined when you try to evaluate len(names).

Using range when you could use enumerate is a bit of anti-pattern anyway; try

Source https://stackoverflow.com/questions/66046886

QUESTION

Can the walrus operator be used to avoid multiple function calls within a list comprehension?

Asked 2021-Feb-04 at 08:35

Let's say I have a list of lists like this

...

ANSWER

Answered 2021-Jan-31 at 16:30

Yes. This is what you want

Source https://stackoverflow.com/questions/65981435

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

Vulnerabilities

No vulnerabilities reported

Install walrus

There are two options for installing and using walrus: install walrus and its dependencies natively on your system, or use our walrus Docker image. It may sound a bit silly to have a Docker container orchestrate other containers, but by sharing the Docker socket (/var/run/docker.sock) with the walrus container it works! There are drawbacks to sharing the Docker socket and we only encourage this approach if you want to try out walrus without thinking about setting up your own environment.

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 .

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