https://github.com/animesh/ngless

NGLess: NGS with less work

https://github.com/animesh/ngless

Repository

NGLess: NGS with less work

https://github.com/animesh/ngless/blob/master/

# NGLess: NGS Processing with Less Work

![NGLess logo](NGLess-logo-128x64.png) Ngless is a domain-specific language for
NGS (next-generation sequencing data) processing.

[![Build Status](https://travis-ci.com/ngless-toolkit/ngless.svg?branch=master)](https://travis-ci.com/ngless-toolkit/ngless)
[![MIT licensed](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/hyperium/hyper/master/LICENSE)
[![Install with Bioconda](https://anaconda.org/bioconda/ngless/badges/installer/conda.svg)](https://anaconda.org/bioconda/ngless)
[![Install with Bioconda](https://anaconda.org/bioconda/ngless/badges/downloads.svg)](https://anaconda.org/bioconda/ngless)
[![Citation for NGLess](https://img.shields.io/badge/CITATION-DOI%3A10.1186%252Fs40168--019--0684--8-brightgreen.svg)](https://doi.org/10.1186/s40168-019-0684-8)
[![Join the chat at https://gitter.im/ngless-toolkit](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/ngless-toolkit)


For questions and discussions, please use the [ngless mailing
list](https://groups.google.com/forum/#!forum/ngless).

If you are using NGLess, please cite:

> _NG-meta-profiler: fast processing of metagenomes using NGLess, a
> domain-specific language_ by Luis Pedro Coelho, Renato Alves, Paulo Monteiro,
> Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork, Microbiome (2019)
> [https://doi.org/10.1186/s40168-019-0684-8](https://doi.org/10.1186/s40168-019-0684-8)

![NGLess cartoon](docs/NGLess-cartoon.svg)

## Example

    ngless "1.0"
    input = fastq(['ctrl1.fq','ctrl2.fq','stim1.fq','stim2.fq'])
    input = preprocess(input) using |read|:
        read = read[5:]
        read = substrim(read, min_quality=26)
        if len(read) < 31:
            discard

    mapped = map(input,
                    reference='hg19')
    write(count(mapped, features=['gene']),
            ofile='gene_counts.csv',
            format={csv})

## Installing

See the [install documentation](https://ngless.embl.de/install.html) for more
information.

### Bioconda

The recommended way to install NGLess is through
[bioconda](http://bioconda.github.io):

    conda install -c bioconda ngless 

### Docker

Alternatively, a docker container with NGLess is available at
[docker hub](https://hub.docker.com/r/nglesstoolkit/ngless):

    docker run -v $PWD:/workdir -w /workdir -it nglesstoolkit/ngless:1.0.0 ngless --version

Adapt the mount flags (``-v``) as needed.

### Linux

You can get a [statically linked version of NGless
1.1.1](https://github.com/ngless-toolkit/ngless/releases/download/v1.1.1/NGLess-1.1.1-static-Linux64)
or a [nighly build of the latest development
code](https://gitlab.com/ngless/ngless/builds/artifacts/master/raw/bin/ngless?job=build-and-test-ubuntu).
This should work across a wide range of Linux versions (please
[report](https://github.com/ngless-toolkit/ngless/issues) any issues you encounter):

    curl -L -O https://github.com/ngless-toolkit/ngless/releases/download/v1.1.1/NGLess-1.1.1-static-Linux64
    chmod +x NGLess-1.1.1-static-Linux64
    ./NGLess-1.1.1-static-Linux64

This download bundles bwa, samtools and megahit (also statically linked).

If you want to try one of ngless' builtin modules (motus, specI, ...) you can
download [the full nighly build zip
file](https://gitlab.com/ngless/ngless/builds/artifacts/master/download?job=build-and-test-ubuntu)
which includes them.

### From Source

Installing/compiling from source is also possible. Clone
[https://github.com/ngless-toolkit/ngless](https://github.com/ngless-toolkit/ngless)

#### Dependencies

The simplest way to get an environment will all the dependencies is to use conda:

    conda create -n ngless
    conda activate ngless
    conda config --add channels conda-forge
    conda install stack cairo bzip2 gmp zlib perl wget xz pkg-config make

You should have `gcc` installed (or another C-compiler).

The following sequence of commands should download and build the software

    git clone https://github.com/ngless-toolkit/ngless
    cd ngless
    stack setup
    make

To install, you can use the following command (replace `` with
the directory where you wish to install, default is `/usr/local`):

    make install prefix=

## Running Sample Test Scripts on Local Machine
For Developers who have successfully comiled and installed NGless, running the test scripts in /tests folder would be the next line of action to have the output of sample(small) test cases.

    cd tests
Once in the test directory, select any of the following many test folders(scripts) to run using NGless.
For example, here we would run the "**regression-fqgz**" and the eventually the .ngl file to get a sample output view that can be used for visualizing the software.

    cd regression-fqgz
    ngless ungzip.ngl
After running this script open the newly generated folder "**ungzip.ngl.output_ngless**" and view the template in the **index.html** file.

For developers who have done this much more data-sets for testing purposes can be referenced and used by reading these documentation links:
**[Human Gut Metagenomics Functional & Taxonomic Profiling](https://ngless.embl.de/tutorial-gut-metagenomics.html#)**
**[ Ocean Metagenomics Functional Profiling](https://ngless.embl.de/tutorial-ocean-metagenomics.html)**
**[Ocean Metagenomics Assembly and Gene Prediction](https://ngless.embl.de/tutorial-assembly-gp.html)**

The download might cause network congestion in some machines, however with a compute trade-off the packages can be downloaded easily.
Get more details of the resources **[here](https://ngless.embl.de/resources/Modules/)**.


## More information

- [Full documentation](https://ngless.embl.de/)
- [Frequently Asked Questions (FAQ)](https://ngless.embl.de/faq.html)
- [ngless mailing list](https://groups.google.com/forum/#!forum/ngless)
- [What's new log](https://ngless.embl.de/whatsnew.html)
- [NGless V1.1.0 Release Documentation](https://ngless.embl.de/whatsnew.html#version-1-1-0)

## Authors

- [Luis Pedro Coelho](http://luispedro.org) (email: [coelho@embl.de](mailto:coelho@embl.de)) (on twitter: [@luispedrocoelho](https://twitter.com/luispedrocoelho))
- Paulo Monteiro
-  Renato Alves
- [Ana Teresa Freitas](http://web.tecnico.ulisboa.pt/ana.freitas/)
-  Peer Bork

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