https://github.com/silask/profiler

Fast profiler using mmseqs
https://github.com/silask/profiler

Last synced: about 1 month ago
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Fast profiler using mmseqs

• Host: GitHub
• URL: https://github.com/silask/profiler
• Owner: SilasK
• License: mit
• Created: 2018-12-06T13:53:15.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2023-09-27T13:11:10.000Z (about 1 year ago)
• Last Synced: 2024-11-02T15:02:53.213Z (about 2 months ago)
• Language: Python
• Size: 6.84 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Snakemake workflow: Profiler

[![Snakemake](https://img.shields.io/badge/snakemake-≥5.2-brightgreen.svg)](https://snakemake.bitbucket.io)

[![Build Status](https://travis-ci.org/snakemake-workflows/profiler.svg?branch=master)](https://travis-ci.org/snakemake-workflows/profiler)

This is the template for a new Snakemake workflow. Replace this text with a comprehensive description covering the purpose and domain.

Insert your code into the respective folders, i.e. `scripts`, `rules`, and `envs`. Define the entry point of the workflow in the `Snakefile` and the main configuration in the `config.yaml` file.

## Authors

* Silas Kieser (@silask)

## Usage

### Step 1: Install workflow

If you simply want to use this workflow, download and extract the [latest release](https://github.com/snakemake-workflows/profiler/releases).

If you intend to modify and further develop this workflow, fork this repository. Please consider providing any generally applicable modifications via a pull request.

In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, if available, its DOI (see above).

### Step 2: Configure workflow

Configure the workflow according to your needs via editing the file `config.yaml`.

### Step 3: Execute workflow

Test your configuration by performing a dry-run via

    snakemake -n

Execute the workflow locally via

    snakemake --cores $N

using `$N` cores or run it in a cluster environment via

    snakemake --cluster qsub --jobs 100

or

    snakemake --drmaa --jobs 100

See the [Snakemake documentation](https://snakemake.readthedocs.io) for further details.

## Testing

Tests cases are in the subfolder `.test`. They should be executed via continuous integration with Travis CI.