Metadata-Version: 2.1
Name: galru
Version: 1.0.0
Summary: galru: CRISPR types
Home-page: https://github.com/quadram-institute-bioscience/galru
Author: Andrew J. Page
Author-email: andrew.page@quadram.ac.uk
License: GPLv3
Description: # Galru
        [![Build Status](https://travis-ci.org/quadram-institute-bioscience/galru.svg?branch=master)](https://travis-ci.org/quadram-institute-bioscience/galru)
        [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/quadram-institute-bioscience/galru/blob/master/LICENSE)
        [![Docker Pulls](https://img.shields.io/docker/pulls/andrewjpage/galru.svg)](https://hub.docker.com/r/quadraminstitute/galru)  
        
        ## Contents
          * [Introduction](#introduction)
          * [Installation](#installation)
            * [Ubuntu/Debian](#ubuntudebian)
            * [Docker](#docker)
          * [Usage](#usage)
          * [License](#license)
          * [Feedback/Issues](#feedbackissues)
          * [Citation](#citation)
        
        ## Introduction
        Galru allows for rapid spoligotyping for Mycobacterium tuberculosis directly from long read sequencing. It is fast and accurate. It requires a minimal amount of information to produce a spoligotype, and allows for near real-time typing when used to process sequencing data as it is produced by a Nanopore sequencer. 
        
        
        # Installation
        If you just want to quickly try out the software please try a Docker continer. This software is designed to run on Linux and OSX. It will not run on Windows.
        
        ## Conda
        [![Anaconda-Server Badge](https://anaconda.org/bioconda/galru/badges/latest_release_date.svg)](https://anaconda.org/bioconda/galru)
        [![Anaconda-Server Badge](https://anaconda.org/bioconda/galru/badges/platforms.svg)](https://anaconda.org/bioconda/galru)
        [![Anaconda-Server Badge](https://anaconda.org/bioconda/galru/badges/downloads.svg)](https://anaconda.org/bioconda/galru)
        
        To install Galru, first install [conda with Python3](https://conda.io/en/latest/miniconda.html) then run:
        
        ```
        conda install -c conda-forge -c bioconda galru
        ```
        
        ## Docker
        Install [Docker](https://www.docker.com/).  There is a docker container which gets automatically built from the latest version of Galru. To install it:
        
        ```
        docker pull quadraminstitute/galru
        ```
        
        To use it you would use a command such as this (substituting in your filename/directories), using the example file in this repository:
        ```
        docker run --rm -it -v /path/to/example_data:/example_data quadraminstitute/galru galru /example_data/example_reads.fastq
        ```
        
        # Usage
        
        ## Quick start
        
        ## galru
        
        ```
        usage: galru [options] uncorrected_long_reads.fastq
        
        Spoligotyping from uncorrected long reads
        
        positional arguments:
          input_file            Input FASTQ file of uncorrected long reads (optionally gzipped)
        
        optional arguments:
          -h, --help            show this help message and exit
          --db_dir DB_DIR, -d DB_DIR
                                Base directory for species databases, defaults to bundled (default: None)
          --cas_fasta CAS_FASTA, -c CAS_FASTA
                                Cas gene FASTA file (optionally gzipped), defaults to bundled (default: None)
          --technology {map-ont,map-pb,ava-pb,ava-ont}, -y {map-ont,map-pb,ava-pb,ava-ont}
                                Sequencing technology (default: map-ont)
          --threads THREADS, -t THREADS
                                No. of threads to use (default: 1)
          --output_file OUTPUT_FILE, -o OUTPUT_FILE
                                Output filename, defaults to STDOUT (default: None)
          --extended_results, -x
                                Output extended results (default: False)
          --gene_start_offset GENE_START_OFFSET, -g GENE_START_OFFSET
                                Only count CRISPR reads which cover this base (default: 30)
          --min_mapping_quality MIN_MAPPING_QUALITY, -m MIN_MAPPING_QUALITY
                                Minimum mapping quality score (default: 10)
          --qcov_margin QCOV_MARGIN, -q QCOV_MARGIN
                                Maximum perc coverage difference between CRISPR and read (default: 100)
          --min_bitscore MIN_BITSCORE, -b MIN_BITSCORE
                                Minimum blast bitscore (default: 38)
          --min_identity MIN_IDENTITY, -i MIN_IDENTITY
                                Minimum blast identity (default: 95)
          --species SPECIES, -s SPECIES
                                Species name, use galru_species to see all available (default: Mycobacterium_tuberculosis)
          --debug               Turn on debugging and save intermediate files (default: False)
          --verbose, -v         Turn on verbose output (default: False)
          --version             show program's version number and exit
        ```
        
        
        # License
        Galru is free software, licensed under [GPLv3](https://raw.githubusercontent.com/quadram-institute-bioscience/galru/master/VERSION/LICENSE).
        
        # Feedback/Issues
        Please report any issues or to provide feedback please go to the [issues page](https://github.com/quadram-institute-bioscience/galru/issues). If you make improvements to the software, add databases or extend profiles, please send us the changes though a [pull request](https://github.com/quadram-institute-bioscience/galru/pulls) so that the whole community may benefit from your work.
        
        # Citation
        Coming soon
        
        # Etymology
        [galrú](https://www.teanglann.ie/en/fgb/galr%C3%BA) (Gal-roo) is the word for infection in Irish (Gaeilge). 
        
        # External Dependencies
        ## System
        * grep
        * xargs
        * find 
        * gunzip
        
        ## Conda
        * cd-hit-est (from cd-hit)
        * minced
        * bedtools
        * samtools (1.3 or above)
        * minimap2
        * ncbi-genome-download 
        * blast+
        
        ## Pypi
        * fastaq (from pyfastaq)
        
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Description-Content-Type: text/markdown
