snakepipes | Customizable workflows based on snakemake and python | Genomics library

by maxplanck-ie Python Version: 2.7.3 License: MIT

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

kandi X-RAY | snakepipes Summary

snakepipes is a Python library typically used in Artificial Intelligence, Genomics applications. snakepipes has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

Customizable workflows based on snakemake and python for the analysis of NGS data

Support

Quality

Security

License

Reuse

Support

snakepipes has a low active ecosystem.

It has 327 star(s) with 79 fork(s). There are 18 watchers for this library.

It had no major release in the last 12 months.

There are 22 open issues and 349 have been closed. On average issues are closed in 150 days. There are 3 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of snakepipes is 2.7.3

Quality

snakepipes has 0 bugs and 76 code smells.

Security

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

snakepipes code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

snakepipes 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

snakepipes releases are available to install and integrate.

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

Top functions reviewed by kandi - BETA

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

Common yaml logs
Load configuration file
Remove unwanted keys from a dictionary
Merge two dictionaries
Write configuration to config file
Main entry point
Lists all available genomes
Runs snakemake and clean up the output
Send an email to the pipe
Check for common arguments
Checks if the sample info file is present
Predict chip dictionary based on input pattern
Extract sample names from input files
Parse args and defaults
Loads the genome data
Set defaults and global defaults
Print DAG

Get all kandi verified functions for this library.

snakepipes Key Features

No Key Features are available at this moment for snakepipes.

snakepipes Examples and Code Snippets

No Code Snippets are available at this moment for snakepipes.

Community Discussions

Trending Discussions on snakepipes

How to fix conda "ResolvePackageNotFound" when building a conda recipe

QUESTION

How to fix conda "ResolvePackageNotFound" when building a conda recipe

Asked 2019-Jun-06 at 16:25

I downloaded a conda package from github to bring a few modifications and would like to build this local package in a conda environment and test my changes. The problem is that the building of the recipe fails because conda has a conda.exceptions.ResolvePackageNotFound error stating that it does not detect 2 packages, snakemake and fuzzywuzzy.

Here is the meta.yaml file:

...

ANSWER

Answered 2019-Jun-06 at 16:25

The problem is that you need to add conda channels that have the appropriate packages. You can search at https://anaconda.org for channels that have the packages you need.

In this case, it seems like bioconda has the snakemake package and conda-forge has fuzzywuzzy so you should be able to do

Source https://stackoverflow.com/questions/56474234

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

Vulnerabilities

No vulnerabilities reported

Install snakepipes

You can download it from GitHub.
You can use snakepipes like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

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: