New upstream version 4.2.2 (2871c2f1) · Commits · Debian Med / card-rgi

.travis.yml

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		language: python

		python:
		- "3.5"
		- "3.6"

		before_install:
		- sudo apt-get -qq update
		- sudo apt-get install -y ncbi-blast+ prodigal
		- wget http://github.com/bbuchfink/diamond/releases/download/v0.8.36/diamond-linux64.tar.gz
		- tar xzf diamond-linux64.tar.gz
		- sudo mv diamond /usr/bin

		install:
		- pip install -r requirements.txt
		- pip install .

		script:
		- ./test.sh

Dockerfile

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		# base image (stripped down ubuntu for Docker)
		FROM phusion/baseimage

		# metadata
		LABEL base.image="ubuntu"
		LABEL version="1"
		LABEL software="RGI"
		LABEL software.version="4.0.3"
		LABEL description="Tool to identify resistance genes using the CARD database"
		LABEL website="https://card.mcmaster.ca/"
		LABEL documentation="https://github.com/arpcard/rgi/blob/master/README.rst"
		LABEL license="https://github.com/arpcard/rgi/blob/master/LICENSE"
		LABEL tags="Genomics"

		# maintainer
		MAINTAINER Finlay Maguire <finlaymaguire@gmail.com>

		# install system dependencies
		RUN \
		apt-get update && \
		apt-get install -y git python3 python3-dev python3-pip ncbi-blast+ prodigal wget && \
		wget http://github.com/bbuchfink/diamond/releases/download/v0.8.36/diamond-linux64.tar.gz && \
		tar xvf diamond-linux64.tar.gz && \
		mv diamond /usr/bin

		# install and test rgi
		RUN git clone https://github.com/arpcard/rgi
		WORKDIR rgi/
		RUN pip3 install -r requirements.txt && \
		pip3 install . && \
		bash test.sh

		# sort the database path issue
		RUN pwd
		WORKDIR /usr
		RUN cp /rgi/card_data/card.json /usr/local/lib/python3.5/dist-packages/app/_data/card.json

		# move to workdir
		WORKDIR /data/

		# set rgi executable as cmd to allow overriding
		CMD ["rgi"]

LICENSE

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		1. About the CARD, ARO, and RGI

		The Comprehensive Antibiotic Resistance Database ("CARD") provides data, models, and
		algorithms relating to the molecular basis of antimicrobial resistance. The CARD provides
		curated reference sequences and SNPs organized via the Antibiotic Resistance Ontology
		("ARO"). These data can be browsed on the website or downloaded in a number of formats.
		These data are additionally associated with detection models, in the form of curated
		homology cut-offs and SNP maps, for prediction of resistome from molecular sequences.
		These models can be downloaded or can be used for analysis of genome sequences using the
		Resistance Gene Identifier ("RGI"), either online or as a stand-alone tool.

		The CARD was designed and developed by the laboratories of Drs. Gerry Wright and Andrew G.
		McArthur of McMaster University's Department of Biochemistry & Biomedical Sciences
		(Hamilton, Ontario, Canada) with the help of a global team of collaborators. It is built
		entirely using open source software and tools. This research has been supported by funds
		from the Canadian Foundation for Innovation, Canadian Institutes of Health Research,
		Natural Sciences and Engineering Research Council of Canada, Medical Research Council
		(UK), and Ontario Research Fund, as well as a Cisco Research Chair in Bioinformatics
		supported by Cisco Systems Canada, Inc. (Dr. McArthur), Canada Research Chair (Dr.
		Wright), and Killam Research Fellowship (Dr. Wright).

		2. Trade Marks and Official Marks

		All trade marks used or displayed on the CARD (card.mcmaster.ca) website are registered or
		unregistered trade marks or official marks of McMaster University. Nothing on the website
		should be interpreted to grant any license to use any trade mark or official mark without
		the express written permission of McMaster University.

		3. Copyright and Discliamer

		All of the materials on the website, including but not limited to the CARD, the RGI, and
		the underlying HTML, text, illustration, designs, icons, audio clips, video clips,
		documents, products, software and all other content (the "Materials") are protected by
		copyright and are either owned by McMaster University, provided by the creator for free
		use by the scientific community, or McMaster University has obtained a license to use the
		Materials for their website. Except as noted in the Terms of Use below, specifically
		sections 4 and 5 below, none of the Materials may be copied, reproduced, distributed,
		republished, downloaded, displayed, posted or transmitted in any form or by any means,
		without the prior written consent of McMaster University, or the original creator, where
		applicable.

		The only exception is the distribution of the Resistance Gene Identifier (RGI) software on
		the Conda open source, cross-platform, language-agnostic package manager and environment
		management system (https://conda.io/). Conda users are still required to abid by the Terms
		of Use listed, specifically sections 4 and 5 below.

		To obtain permission to reproduce material on the CARD website, please send a request to:

		McMaster University
		c/o McMaster Industry Liaison Office
		305 – 175 Longwood Rd South
		Hamilton, Ontario L8P 0A1
		Attention: Copyright Advisor
		E: milodsk@mcmaster.ca

		4. Terms of Use for Non-Commercial, Research or Academic Reproduction

		All information and the Materials at CARD has been posted to provide the public with
		direct access to information about Antibiotic Resistance. The information and the
		Materials have been posted with the intent that it be readily available for personal and
		public non-commercial, research or academic use by individuals at academic institutions
		only and except where otherwise prohibited, may be reproduced, in part or in whole and by
		any means, without charge or further permission from McMaster University. Any other
		organization must seek to obtain a license described in section 5 below.

		We only ask that:

		4.1 The Materials not be modified and used "as is"

		4.2 Users exercise due diligence in ensuring the accuracy of the Materials

		4.3 McMaster University be identified as the source of the Materials

		4.4 The reproduction is not represented as an official version of the Materials
		reproduced, nor as having been made in affiliation with or without the endorsement of
		McMaster University

		5. Terms of Use for Commercial or Non-Academic Organizations

		Use or reproduction of Materials on the site, in whole or in part, by any non-academic
		organization whether or not for non-commercial (including research) or commercial purposes
		is prohibited, except with written permission of McMaster University. Commercial uses of
		the Materials on the site are offered only pursuant to a written license and user fee. To
		obtain permission and begin the licensing process, please contact McMaster University
		using the address in section 3.

		6. Disclaimer

		The Materials on this site are provided "as is" without warranties or conditions of any
		kind either expressed or implied. To the fullest extent possible under applicable law,
		McMaster University disclaims all warranties and conditions, expressed or implied,
		including but not limited to, implied warranties or conditions of merchantability and
		fitness for a particular purpose, non-infringement or other violation of rights. McMaster
		University does not warrant or make any other representations regarding the use, accuracy,
		timelines, applicability, performance, security, availability or reliability of this
		website or any of the sites linked to this website, or the results from the use of this
		website or any sites linked to this website, or otherwise respecting the Materials on this
		website or any sites linked to this website.

		7. Limitation of Liability

		Under no circumstances, including but not limited to negligence, shall McMaster University
		be liable for any direct, indirect, special, punitive, incidental or consequential damages
		arising out of the use of, or the inability to use, the website or the Materials.

README.rst

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		Resistance Gene Identifier (RGI)
		--------------------------------------------

		This application is used to predict resistome(s) from protein or nucleotide data based on homology and SNP models. The application uses data from `CARD database <https://card.mcmaster.ca/>`_.

		.. image:: https://travis-ci.org/arpcard/rgi.svg?branch=master
		:target: https://travis-ci.org/arpcard/rgi

		Table of Contents
		-------------------------------------

		- `License`_
		- `Requirements`_
		- `Install dependencies`_
		- `Install RGI from project root`_
		- `Running RGI tests`_
		- `Help menu`_
		- `Usage`_
		- `Load card.json`_
		- `Check database version`_
		- `Run RGI`_
		- `Run RGI using GNU parallel`_
		- `Running RGI with short contigs to predict partial genes`_
		- `Clean previous or old databases`_
		- `RGI Heatmap`_
		- `Run RGI from docker`_
		- `Tab-delimited results file`_
		- `Support & Bug Reports`_



		License
		--------
		Use or reproduction of these materials, in whole or in part, by any non-academic organization whether or not for non-commercial (including research) or commercial purposes is prohibited, except with written permission of McMaster University. Commercial uses are offered only pursuant to a written license and user fee. To obtain permission and begin the licensing process, see `CARD website <https://card.mcmaster.ca/about>`_

		Requirements
		--------------------

		- `Prodigal v2.6.3 <https://github.com/hyattpd/prodigal/wiki/Installation>`_
		- `NCBI BLAST v2.6.0+ <https://blast.ncbi.nlm.nih.gov/Blast.cgi>`_
		- `DIAMOND v0.8.36 <https://ab.inf.uni-tuebingen.de/software/diamond>`_
		- `Python 3.6 <https://www.python.org/>`_

		Install dependencies
		--------------------

		- pip3 install biopython
		- pip3 install filetype
		- pip3 install pandas
		- pip3 install pytest
		- pip3 install mock

		Install RGI from project root
		-----------------------------

		.. code-block:: sh

		pip3 install .

		or

		.. code-block:: sh

		python3 setup.py build
		python3 setup.py test
		python3 setup.py install

		Running RGI tests
		-------------------
		.. code-block:: sh

		cd tests
		pytest -v -rxs

		Help menu
		-------------------

		.. code-block:: sh

		rgi --help

		Usage
		-------------------

		.. code-block:: sh

		usage: rgi <command> [<args>]
		commands are:
		main Runs rgi application
		tab Creates a Tab-delimited from rgi results
		parser Creates categorical JSON files RGI wheel visualization
		load Loads CARD database JSON file
		clean Removes BLAST databases and temporary files
		galaxy Galaxy project wrapper
		database Information on installed card database
		heatmap Heatmap for multiple analysis
		---------------------------------------------------------------------------------------
		bwt Metagenomics resistomes (Experimental)
		card_annotation Create fasta files with annotations from card.json (Experimental)
		wildcard_annotation Create fasta files with annotations from variants (Experimental)
		baits_annotation Create fasta files with annotations from baits (Experimental)
		remove_duplicates Removes duplicate sequences (Experimental)
		kmer_build Build CARD*kmer database (Experimental)
		kmer_query Query sequences through CARD*kmers (Experimental)

		Resistance Gene Identifier - <version_number>

		positional arguments:
		command Subcommand to run

		optional arguments:
		-h, --help show this help message and exit

		Use the Resistance Gene Identifier to predict resistome(s) from protein or
		nucleotide data based on homology and SNP models. Check
		https://card.mcmaster.ca/download for software and data updates. Receive email
		notification of monthly CARD updates via the CARD Mailing List
		(https://mailman.mcmaster.ca/mailman/listinfo/card-l)


		Load card.json
		-------------------

		- local or working directory

		.. code-block:: sh

		rgi load --afile /path/to/card.json --local

		- system wide

		.. code-block:: sh

		rgi load --afile /path/to/card.json

		Check database version
		-----------------------

		- local or working directory

		.. code-block:: sh

		rgi database --version --local

		- system wide

		.. code-block:: sh

		rgi database --version

		Run RGI
		----------------------

		- local or working directory

		.. code-block:: sh

		rgi main --input_sequence /path/to/protein_input.fasta --output_file /path/to/output_file --input_type protein --local

		- system wide

		.. code-block:: sh

		rgi main --input_sequence /path/to/nucleotide_input.fasta --output_file /path/to/output_file --input_type contig

		Run RGI using GNU parallel
		--------------------------------------------

		- system wide and writing log files for each input file. (Note add code below to script.sh then run with `./script.sh /path/to/input_files`)

		.. code-block:: sh

		#!/bin/bash
		DIR=`find . -mindepth 1 -type d`
		for D in $DIR; do
		NAME=$(basename $D);
		parallel --no-notice --progress -j+0 'rgi main -i {} -o {.} -n 16 -a diamond --clean --debug > {.}.log 2>&1' ::: $NAME/*.{fa,fasta};
		done



		Running RGI with short contigs to predict partial genes
		--------------------------------------------------------

		- local or working directory

		.. code-block:: sh

		rgi main --input_sequence /path/to/nucleotide_input.fasta --output_file /path/to/output_file --local --low_quality

		- system wide

		.. code-block:: sh

		rgi main --input_sequence /path/to/nucleotide_input.fasta --output_file /path/to/output_file --low_quality


		Clean previous or old databases
		--------------------------------

		- local or working directory

		.. code-block:: sh

		rgi clean --local

		- system wide

		.. code-block:: sh

		rgi clean

		RGI Heatmap
		------------

		- Default Heatmap

		.. code-block:: sh

		rgi heatmap --input /path/to/rgi_results_json_files_directory/

		- Heatmap with `AMR Gene Family` categorization

		.. code-block:: sh

		rgi heatmap --input /path/to/rgi_results_json_files_directory/ --category gene_family

		- Heatmap with `AMR Gene Family` categorization and fill display

		.. code-block:: sh

		rgi heatmap --input /path/to/rgi_results_json_files_directory/ --category gene_family --display fill

		- Heatmap with `AMR Gene Family` categorization and coloured y-axis labels display

		.. code-block:: sh

		rgi heatmap --input /path/to/rgi_results_json_files_directory/ --category gene_family --display text


		- Heatmap with frequency display enabled

		.. code-block:: sh

		rgi heatmap --input /path/to/rgi_results_json_files_directory/ --frequency

		- Heatmap with drug class category and frequency enabled

		.. code-block:: sh

		rgi heatmap --input /path/to/rgi_results_json_files_directory/ --category drug_class --frequency --display text

		- Heatmap with samples and genes clustered

		.. code-block:: sh

		rgi heatmap --input /path/to/rgi_results_json_files_directory/ --cluster both

		- Heatmap with resistance mechanism categorization and clustered samples

		.. code-block:: sh

		rgi heatmap --input /path/to/rgi_results_json_files_directory/ --cluster samples --category resistance_mechanism --display fill


		Run RGI from docker
		-------------------

		- First you you must either pull the docker container from dockerhub (latest CARD version automatically installed)

		.. code-block:: sh

		docker pull finlaymaguire/rgi

		- Or Alternatively, build it locally from the Dockerfile (latest CARD version automatically installed)

		.. code-block:: sh

		git clone https://github.com/arpcard/rgi
		docker build -t arpcard/rgi rgi

		- Then you can either run interactively (mounting a local directory called `rgi_data` in your current directory
		to `/data/` within the container

		.. code-block:: sh

		docker run -i -v $PWD/rgi_data:/data -t arpcard/rgi bash

		- Or you can directly run the container as an executable with `$RGI_ARGS` being any of the commands described above. Remember paths to input and outputs files are relative to the container (i.e. `/data/` if mounted as above).

		.. code-block:: sh

		docker run -v $PWD/rgi_data:/data arpcard/rgi $RGI_ARGS

		Tab-delimited results file
		---------------------------

		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| ORF_ID \| Open Reading Frame identifier (internal to RGI)\|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| Contig \| Source Sequence \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| Start \| Start co-ordinate of ORF \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| Stop \| End co-ordinate of ORF \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| Orientation \| Strand of ORF \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| Cut_Off \| RGI Detection Paradigm \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| Pass_Bitscore \| STRICT detection model bitscore value cut-off \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| Best_Hit_Bitscore \| Bitscore value of match to top hit in CARD \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| Best_Hit_ARO \| ARO term of top hit in CARD \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| Best_Identities \| Percent identity of match to top hit in CARD \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| ARO \| ARO accession of top hit in CARD \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| Model_type \| CARD detection model type \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| \| Mutations observed in the ARO term of top hit \|
		\| SNPs_in_Best_Hit_ARO \| in CARD (if applicable) \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| \| Mutations observed in ARO terms of other hits \|
		\| Other_SNPs \| indicated by model id (if applicable) \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| Drug Class \| ARO Categorization \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| Resistance Mechanism \| ARO Categorization \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| AMR Gene Family \| ARO Categorization \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| Predicted_DNA \| ORF predicted nucleotide sequence \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| Predicted_Protein \| ORF predicted protein sequence \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| CARD_Protein_Sequence \| Protein sequence of top hit in CARD \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| Calculated as percentage \|
		\| \| (length of ORF protein / \|
		\| Percentage Length of Reference Sequence \| length of CARD reference protein) \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| ID \| HSP identifier (internal to RGI) \|
		+----------------------------------------------------------+------------------------------------------------+
		\| :: \| \|
		\| Model_id \| CARD detection model id \|
		+----------------------------------------------------------+------------------------------------------------+



		Support & Bug Reports
		----------------------

		Please log an issue on `github issue <https://github.com/arpcard/rgi/issues>`_.

		You can email the CARD curators or developers directly at `card@mcmaster.ca <mailto:card@mcmaster.ca>`_, via Twitter at `@arpcard <http://www.twitter.com/arpcard>`_.

_data/.gitignore

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		card.json
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