MOSCA | Meta-Omics Software for Community Analysis | Genomics library

by iquasere Python Version: 2.1.0 License: GPL-3.0

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

kandi X-RAY | MOSCA Summary

MOSCA is a Python library typically used in Institutions, Learning, Administration, Public Services, Artificial Intelligence, Genomics applications. MOSCA has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. However MOSCA build file is not available. You can download it from GitHub.

MOSCA (portuguese for fly) is a pipeline designed for performing metagenomics (MG) and metatranscriptomics (MT) integrated data analyses, in a mostly local and fully automated workflow.

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Quality

Security

License

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Support

MOSCA has a low active ecosystem.

It has 30 star(s) with 4 fork(s). There are 4 watchers for this library.

It had no major release in the last 12 months.

There are 1 open issues and 16 have been closed. On average issues are closed in 118 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of MOSCA is 2.1.0

Quality

MOSCA has no bugs reported.

Security

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

License

MOSCA is licensed under the GPL-3.0 License. This license is Strong Copyleft.

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

Reuse

MOSCA releases are available to install and integrate.

MOSCA has no build file. You will be need to create the build yourself to build the component from source.

Installation instructions, examples and code snippets are available.

Top functions reviewed by kandi - BETA

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

Run the database generation
Run a bash command
Perform a Compatibility workflow
Browse results of peptide - Shapeshaker - Shaker - Shapes
Run fastqc
Perform quality trim
Download rRNA databases
Parse a fastqc report
Run preCOGnizer
Parse command line arguments
Add abundance counts
Write data to Excel file
Make a protein report from the RECIMAPI results
Build a GFF file from a sequence of sequences
Count the spectra for each protein report
Run checks
Save configuration data to file
Build a gff file from contigs
Run gene calling
Read config file
Remove censored input data
Run analysis
Run experiment
Make an entry report for each entry
Run assembler
Return human readable time

Get all kandi verified functions for this library.

MOSCA Key Features

No Key Features are available at this moment for MOSCA.

MOSCA Examples and Code Snippets

No Code Snippets are available at this moment for MOSCA.

Community Discussions

Trending Discussions on MOSCA

Connecting to MongoDB - Command 'createIndexes' requires authentication (Maybe Agenda.js related?)

Run snakemake rules iteratively

Converting a large pipeline to snakemake

Node.js - Mosca & Heroku

clean a badly-encoded text in Python

How to connect our callback function to the mosca authenticate method?

How to dynamically use a form in javascript code

Nodejs - Express - Socket.io How to send a message to a specific socket.id from an outside function?

Nodejs Safe MQTT Connection

Django how to display subquerys in Template

QUESTION

Connecting to MongoDB - Command 'createIndexes' requires authentication (Maybe Agenda.js related?)

Asked 2021-Apr-20 at 16:48

As I'm introducing authentication for my MongoDB instance in Docker, I ran into problems which are probably related to the way agenda.js tries to connect to MongoDB, as the connection string invokes successful logs for mongoose connecting to the DB, therefore I assume the string should be valid.

Everything worked until I changed the connection string to use authentication. I verified the users are properly created in the database and also tried variations of the connection string and deleting/installing node modules.

Following output I get upon running docker-compose up:

...

ANSWER

Answered 2021-Apr-20 at 16:48

try this

workaround these deprecation warnings with Mongoose provided options

Source https://stackoverflow.com/questions/67158764

QUESTION

Run snakemake rules iteratively

Asked 2020-Oct-19 at 17:52

So I thought I was finally grasping snakemake, but when trying to run several different data files, I realized it doesn't work as I though. This is the Snakefile:

...

ANSWER

Answered 2020-Oct-19 at 17:52

This is a very common mistake. The thing to remember is that rules should work for a single sample. Snakemake will take your paths (with wildcards) and generate specific jobs from the rules. You've written something that takes all inputs and all outputs, then I presume, preprocess.py expects one input/output.

Instead, consider one file at a time. For the output, "{output}/Preprocess/Trimmomatic/quality_trimmed_{name}{fr}.fq", how do you generate that file? You would have to match to an input file in your experiments dataframe using the name as a key.

Source https://stackoverflow.com/questions/64429848

QUESTION

Converting a large pipeline to snakemake

Asked 2020-Oct-15 at 16:59

I have developed MOSCA, a pipeline for meta-omics analysis (MG with MT), which is available through Bioconda. I want to convert it to snakemake, since it would easily allow MOSCA to run simultaneously some accesses through APIs and some computationally demanding tasks. Also, I think it would help better shape the tool to a standard format.

My question is, MOSCA has a lot of parameters, which will have to be transfered to a configuration file. While this is trivial for most parameters, inputting MG and MT files together is trickier. Also, MOSCA considers samples together. So I created a samples' file, samples.tsv

...

ANSWER

Answered 2020-Oct-14 at 09:50

I'm not sure what you are trying to do but to me the line

Source https://stackoverflow.com/questions/64340217

QUESTION

Node.js - Mosca & Heroku

Asked 2020-Sep-21 at 09:44

I built a server on node.js that use Mosca and MQTT.

On my localhost everything worked find, including get/send messages via mosquitto (_sub/_pub).

When I uploaded the code to Heroku, the mqtt request worked inside the server, but I saw nothing on mosquitto.

That is my code to run the MQTT broker.

...

ANSWER

Answered 2020-Sep-21 at 09:44

Heroku will only expose a web app via HTTP (on port 80 or 443 for HTTPS). It will not forward incoming data on port 1883 to the application instance.

If you leave mosquitto_sub long enough I expect it will print an error about failing to connect.

If you want to host a MQTT broker on Heroku you will need to use MQTT over Websockets most likely with HTTPS on port 443

Source https://stackoverflow.com/questions/63988192

QUESTION

clean a badly-encoded text in Python

Asked 2020-May-16 at 11:52

I have some texts in a Pandas dataframe (in a specific column called text)

here an abstract (converted to list):

...

ANSWER

Answered 2020-May-16 at 11:52

def string_cleaner(rouge_text):
    return ("".join(rouge_text.strip()).encode('ascii', 'ignore').decode("utf-8"))

Source https://stackoverflow.com/questions/61835734

QUESTION

How to connect our callback function to the mosca authenticate method?

Asked 2020-May-02 at 11:18

var mqtt = require('mqtt')
var options = {
  username: 'abc',
  password: 'xyz',
}
var client  = mqtt.connect('mqtt:localhost:1883', options);

function authenteClient() {
      // I need to call this function against the callback at server's 
      // authenticate function.
}

...

ANSWER

Answered 2018-Apr-19 at 06:44

If the client fails the authentication on the broker side it will not connect.

If it passes it will connect and you can be notified by using the client.on('connect',function(){}) event listener.

Source https://stackoverflow.com/questions/49914017

QUESTION

How to dynamically use a form in javascript code

Asked 2020-Apr-27 at 16:46

I would like to know how I can call a function using the dynamic result of what I typed in a form! I managed to transform this value to be used but when I press the button it doesn't change and stays statically at 0 (as if I hadn't typed anything)

HTML:

...

ANSWER

Answered 2020-Apr-27 at 16:44

Put your JavaScript code inside a function so it can be called later in time

Source https://stackoverflow.com/questions/61463688

QUESTION

Nodejs - Express - Socket.io How to send a message to a specific socket.id from an outside function?

Asked 2020-Mar-26 at 01:09

I'm having problem finding the right answer for this. I'm trying to send a message to a specific socket.id given I'm handling multiple users but I need to do it from another function which does not have access to socket.io.

I need to send the message to the specific socket.id inside the function:

...

ANSWER

Answered 2020-Mar-26 at 01:09

First off, the way you send to a specific socket id is with this:

Source https://stackoverflow.com/questions/60858665

QUESTION

Nodejs Safe MQTT Connection

Asked 2019-Oct-28 at 11:34

On my server I'm using a node.js based mqtt broker (mosca) which has an SSL Certificate from Certbot.

On the client side, I'm using a node.js based solution as well (mqtt.js)

Now my question is: In order to have a safe connection, do I need to have the property rejectUnauthorized: true? Because I can only get it to work when having a self signed certificate, which of course isn't very secure. When having a regular SSL cert on server-side i can't get it to work having rejectUnauthorized: true, why?

My server options:

...

ANSWER

Answered 2019-Oct-28 at 11:34

Update your server side settings to point to the fullchain.pem rather than the cert.pem file

This will include the full trust chain in what the server presents which should then include the root CA cert that will be in the trusted set that is baked into NodeJS.

Source https://stackoverflow.com/questions/58587671

QUESTION

Django how to display subquerys in Template

Asked 2019-Oct-02 at 00:08

My view:

...

ANSWER

Answered 2019-Oct-01 at 23:51

The returned values are tuples. You can access them using indices, for example:

Source https://stackoverflow.com/questions/58193624

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

Vulnerabilities

No vulnerabilities reported

Install MOSCA

MOSCA files can be retrieved from git. MOSCA requires Conda previously installed. Instructions on installing Anaconda on an Ubuntu 18.04 may be found here. Alternatively, you can directly download the installation for Ubuntu with which MOSCA was tested - problems have been found using more recent distributions.
To use MOSCA through Bioconda, an environment must be created containing all the dependencies. Create the environment and install MOSCA with. Activate the environment with.

Support

MOSCA (portuguese for fly) is a pipeline designed for performing metagenomics (MG) and metatranscriptomics (MT) integrated data analyses, in a mostly local and fully automated workflow.

Find more information at: