swarm | fast clustering method for amplicon-based studies | Genomics library

by torognes C++ Version: v3.1.0 License: AGPL-3.0

X-Ray Key Features Code Snippets(1)Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | swarm Summary

swarm is a C++ library typically used in Artificial Intelligence, Genomics, Example Codes applications. swarm has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

A robust and fast clustering method for amplicon-based studies. The purpose of swarm is to provide a novel clustering algorithm that handles massive sets of amplicons. Results of traditional clustering algorithms are strongly input-order dependent, and rely on an arbitrary global clustering threshold. swarm results are resilient to input-order changes and rely on a small local linking threshold d, representing the maximum number of differences between two amplicons. swarm forms stable, high-resolution clusters, with a high yield of biological information. To help users, we describe a complete pipeline starting from raw fastq files, clustering with swarm and producing a filtered occurrence table.

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Quality

Security

License

Reuse

Support

swarm has a low active ecosystem.

It has 90 star(s) with 20 fork(s). There are 14 watchers for this library.

It had no major release in the last 12 months.

There are 5 open issues and 156 have been closed. On average issues are closed in 131 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of swarm is v3.1.0

Quality

swarm has no bugs reported.

Security

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

License

swarm is licensed under the AGPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

swarm releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

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swarm Key Features

No Key Features are available at this moment for swarm.

swarm Examples and Code Snippets

String representation of a swarm .

java

Lines of Code : 5

License : Permissive (MIT License)

Copy

@Override
	public String toString() {
		return "Swarm [particles=" + Arrays.toString(particles) + ", bestPosition=" + Arrays.toString(bestPosition)
				+ ", bestFitness=" + bestFitness + ", random=" + random + "]";
	}

Community Discussions

Trending Discussions on swarm

Hasura query action exception

“500 Internal Server Error” with job artifacts on minio

Traefik: Load Balance Across Three Node Docker Swarm

Soft restart daemon containers in docker swarm

Cannot connect to the Docker daemon via docker-sdk golang

How can I display kind="swarm" and kind="point" on the same catplot in Seaborn?

How to copy files inside a local virtual machine or how to edit a yml file inside a local virtual machine? (docker stack)

Cannot add web3 to React project

Application deployed to Docker Swarm is not connecting with MongoDB Replica Set

Unwanted Warm Shutdown (MainProcess) of node worker in airflow docker swarm

QUESTION

Hasura query action exception

Asked 2021-Jun-14 at 19:30

Got a small problem (I guess). I created c# rest web API on docker swarm environment. Rest API is working properly - tested via the postman. Then I tried to compose Hasura service on the same docker swarm environment. The console is working properly also. The problem is with query action.

Code:

Action definition:

...

ANSWER

Answered 2021-Jun-14 at 19:30

No, currently it's not possible, Hasura always makes POST requests to the action handler:

When the action is executed i.e. when the query or the mutation is called, Hasura makes a POST request to the handler with the action arguments and the session variables.

Source: https://hasura.io/docs/latest/graphql/core/actions/action-handlers.html#http-handler

Source https://stackoverflow.com/questions/67971639

QUESTION

“500 Internal Server Error” with job artifacts on minio

Asked 2021-Jun-14 at 18:30

I'm running gitlab-ce on-prem with min.io as a local S3 service. CI/CD caching is working, and basic connectivity with the S3-compatible minio is good. (Versions: gitlab-ce:13.9.2-ce.0, gitlab-runner:v13.9.0, and minio/minio:latest currently c253244b6fb0.)

Is there additional configuration to differentiate between job-artifacts and pipeline-artifacts and storing them in on-prem S3-compatible object storage?

In my test repo, the "build" stage builds a sparse R package. When I was using local in-gitlab job artifacts, it succeeds and moves on to the "test" and "deploy" stages, no problems. (And that works with S3-stored cache, though that configuration is solely within gitlab-runner.) Now that I've configured minio as a local S3-compatible object storage for artifacts, though, it fails.

...

ANSWER

Answered 2021-Jun-14 at 18:30

The answer is to bypass the empty-string test; the underlying protocol does not support region-less configuration, nor is there a configuration option to support it.

The trick is able to work because the use of 'endpoint' causes the 'region' to be ignored. With that, setting the region to something and forcing the endpoint allows it to work:

Source https://stackoverflow.com/questions/67005428

QUESTION

Traefik: Load Balance Across Three Node Docker Swarm

Asked 2021-Jun-13 at 03:53

I am working on setting up a three node Docker swarm for a web application I support. Initially, we have Traefik setup as a reverse proxy. Traefik and the web app both run on the same web server and the web server is in a single node docker swarm. We are trying to add two additional nodes for application stability.

At the moment, I'm simply trying to understand Traefik load balancing along with Docker Swarm. I am deploying a Traefik v1.7 stack and including the whoami application. The docker-compose file for this first past looks like:

...

ANSWER

Answered 2021-Jun-13 at 03:53

Apparently Traefik can't drain the connections during update (maybe it doesn't have access to healthchecks and swarm info?).

To achieve a zero-downtime rolling update you should delegate the load-balancing to docker swarm itself:

Source https://stackoverflow.com/questions/66536125

QUESTION

Soft restart daemon containers in docker swarm

Asked 2021-Jun-11 at 20:48

we use multiple PHP workers. Every PHP worker is organized in one container. To scale the amount of parallel working processes we handle it in a docker swarm.

So the PHP is running in a loop and waiting for new jobs (Get jobs from Gearman). If a new job is receiving, it would be processed. After that, the script is waiting for the next job without quitting/leaving the PHP script.

Now we want to update our workers. In this case, the image is the same but the PHP script is changed. So we have to leave the PHP script, update the PHP script file, and restart the PHP script.

If I use this docker service update command. Docker will stop the container immediately. In the worst case, a running worker will be canceled during this work.

...

ANSWER

Answered 2021-Jun-11 at 20:48

In the meantime, we have solved it with SIGNALS.

In PHP work with signals is very easy. In our case, this structure helped us.

Source https://stackoverflow.com/questions/67586385

QUESTION

Cannot connect to the Docker daemon via docker-sdk golang

Asked 2021-Jun-08 at 20:40

Docker is running, ContainerExecCreate creates a container, but ContainerExecAttach returns: Cannot connect to the Docker daemon at unix: ///var/run/docker.sock in response. Is the docker daemon running?

What could be the problem.

...

ANSWER

Answered 2021-Jun-08 at 20:40

It looks normal. May depend on the state of the docker at the time of the call. It is possible to check docker via Ping or just wait one second.

Source https://stackoverflow.com/questions/67791022

QUESTION

How can I display kind="swarm" and kind="point" on the same catplot in Seaborn?

Asked 2021-Jun-04 at 14:16

I am trying to display both the means and errors (kind="point") and individual data points (kind="swarm") overlayed on the same catplot in Seaborn.

I have the following code:

...

ANSWER

Answered 2021-Jun-04 at 14:16

Using a face grid, you can overlay each one by specifying each one with map_dataframe(). The examples in this official reference have been modified. The data is based on sample data.

Source https://stackoverflow.com/questions/67837930

QUESTION

How to copy files inside a local virtual machine or how to edit a yml file inside a local virtual machine? (docker stack)

Asked 2021-Jun-03 at 10:23

I'm following a tutorial on docker stack, swarm, compose, etc.

the teacher connects to a VM of the swarm and then deploys a docker stack from this directory docker@node1:~/srv/swarm-stack-1:

...

ANSWER

Answered 2021-Jun-03 at 10:23

SOLVED

The solution here is not to ssh into the VM, and instead to change to the VM context with:

Source https://stackoverflow.com/questions/67785971

QUESTION

Cannot add web3 to React project

Asked 2021-Jun-03 at 00:31

I'm trying to add Web3 to a React project. I've initalized a new project with

...

ANSWER

Answered 2021-Apr-26 at 09:19

Unfortunately, most of the Web3 stack relies heavily on window, browser and external, crypto dependencies which aren't available on server-side. This isn't just an issue with Gatsby, but other SSR and static site generators (e.g. Next.js) as well.

There are a few workarounds though. See Using Client-Side Only Packages on Gatsby

Use a different library or approach
Add client-side package via CDN
Load client-side dependent components with loadable-components
Use React.lazy and Suspense on client-side only

Depending on your requirements #1 is likely not an option. I've had better success using ethers, instead of web3. But you'll likely run into similar issues with other packages at some point.

A combination of #2 and 3/4 will be the way to go. First, remove the packages (web3) that are causing issues and load them either from gatsby-browser.js or using react-helmet on the page/component that's using it.

gatsby-browser.js

Source https://stackoverflow.com/questions/66952972

QUESTION

Application deployed to Docker Swarm is not connecting with MongoDB Replica Set

Asked 2021-Jun-02 at 10:18

I have deployed my application using Docker Swarm with 3 machines.

MongoDB Replica Set is configured manually and its working as a service on Ubuntu machine.

I am trying to connect to my Backend application to MongoDB Replica Set but I am getting context deadline exceeded error. I am using Private-ip to connect since machines are in same AWS VPC. Port 27017 is open in the security group and can be used by VPC network IP.

/etc/hosts is correctly configured on every machine.

I am using Docker-Compose file to deploy the stack.

Replica Set is working fine. I have checked it with manually inserting few documents.

The picture will help readers to understand the context better.

Abbreviations

BE = Backend
FE = Frontend
Mac 1 = Machine 1
AZ-1 = Availability Zone 1
VPC = Virtual Private Cloud

My Guess:
Is it because Replica-Set in not in the Swarm Network and that's why its unable to connect ???

I am trying to fix this issue for quite sometime now and have not been successful yet. Help is required now.

...

ANSWER

Answered 2021-Jun-02 at 10:18

I found the solution.

The problem was related to the names of the MongoDB replica instances.

The host name for first member is "host" : "10.0.0.223:27017"
The host name for second member is "host" : "node2:27017"
The host name for third member is "host" : "node3:27017"

Due to this inconsistency, the backend application was not able to connect to the replica set.

Source https://stackoverflow.com/questions/67751750

QUESTION

Unwanted Warm Shutdown (MainProcess) of node worker in airflow docker swarm

Asked 2021-May-31 at 13:50

I am currently setting up remote workers via docker swarm for Apache Airflow on AWS EC2 instances.

A remote worker shuts down every 60 seconds without an apparent reason with the following error:

...

ANSWER

Answered 2021-May-31 at 13:50

just wanted to let you know that I was able to fix the issue by setting CELERY_WORKER_MAX_TASKS_PER_CHILD=500, which otherwise defaults to 50. Our Airflow DAG was sending around 85 tasks to this worker, so it was probably overwhelmed.

Apparently celery doesn't accept more incoming messages from redis and redis shuts down the worker if its outgoing message pipeline is full.

After searching for days with two people, we found the answer. Apparently it is still a workaround, but it works as is should now. I found the answer in this github issue. Just wanted to let you know.

If you have further insights please feel free to share.

Source https://stackoverflow.com/questions/67707342

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

Vulnerabilities

No vulnerabilities reported

Install swarm

swarm most simple usage is:.
Get the latest binaries for GNU/Linux, macOS or Windows from the release page. Get the source code from GitHub using the ZIP button or git, and compile swarm:.
(thanks to GitHub user Gian77 for reporting this procedure).

Support

To facilitate the use of swarm, we provide examples of options or shell commands that can be use to parse swarm's output. We assume that the amplicon fasta file was prepared as describe above (linearization and dereplication).

Find more information at: