Tree @upstream/2.12.1+ds (Download .tar.gz)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 | # ARIBA Antimicrobial Resistance Identification By Assembly For how to use ARIBA, please see the [ARIBA wiki page][ARIBA wiki]. [![Build Status](https://travis-ci.org/sanger-pathogens/ariba.svg?branch=master)](https://travis-ci.org/sanger-pathogens/ariba) [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/ariba/blob/master/LICENSE) [![status](https://img.shields.io/badge/MGEN-10.1099%2Fmgen.0.000131-brightgreen.svg)](http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000131) ## Contents * [Introduction](#introduction) * [Quick Start](#quick-start) * [Installation](#installation) * [Required dependencies](#required-dependencies) * [Using pip3](#using-pip3) * [From Source](#from-source) * [Docker](#docker) * [Debian (testing)](#debian-testing) * [Ubuntu](#ubuntu) * [Dependencies and environment variables](#dependencies-and-environment-variables) * [Temporary files](#temporary-files) * [Usage](#usage) * [License](#license) * [Feedback/Issues](#feedbackissues) * [Citation](#citation) ## Introduction ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies. It can also be used for [MLST calling](https://github.com/sanger-pathogens/ariba/wiki/MLST-calling-with-ARIBA). The input is a FASTA file of reference sequences (can be a mix of genes and noncoding sequences) and paired sequencing reads. ARIBA reports which of the reference sequences were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference sequences. ## Quick Start Get reference data, for instance from [CARD](https://card.mcmaster.ca/). See [getref](https://github.com/sanger-pathogens/ariba/wiki/Task%3A-getref) for a full list. ariba getref card out.card Prepare reference data for ARIBA: ariba prepareref -f out.card.fa -m out.card.tsv out.card.prepareref Run local assemblies and call variants: ariba run out.card.prepareref reads1.fastq reads2.fastq out.run Summarise data from several runs: ariba summary out.summary out.run1/report1.tsv out.run2/report2.tsv out.run3/report3.tsv Please read the [ARIBA wiki page][ARIBA wiki] for full usage instructions. ## Installation If you encounter an issue when installing ARIBA please contact your local system administrator. If you encounter a bug please log it [here](https://github.com/sanger-pathogens/ariba/issues) or email us at ariba-help@sanger.ac.uk. ### Required dependencies * [Python3][python] version >= 3.3.2 * [Bowtie2][bowtie2] version >= 2.1.0 * [CD-HIT][cdhit] version >= 4.6 * [MUMmer][mummer] version >= 3.23 ARIBA also depends on several Python packages, all of which are available via pip. Installing ARIBA with pip3 will get these automatically if they are not already installed: * dendropy >= 4.2.0 * matplotlib (no minimum version required, but only tested on 2.0.0) * pyfastaq >= 3.12.0 * pysam >= 0.9.1 * pymummer >= 0.10.1 ### Using pip3 Install ARIBA using pip: pip3 install ariba ### From Source Download the latest release from this github repository or clone it. Run the tests: python3 setup.py test If the tests all pass, install: python3 setup.py install ### Docker ARIBA can be run in a Docker container. First install Docker, then install ARIBA: docker pull sangerpathogens/ariba To use ARIBA use a command like this (substituting in your directories), where your files are assumed to be stored in /home/ubuntu/data: docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/ariba ariba -h ### Debian (testing) ARIBA is available in the latest version of Debian, and over time will progressively filter through to Ubuntu and other distributions which use Debian. To install it as root: sudo apt-get install ariba ### Ubuntu You can use `apt-get` (see above), or to ensure you get the latest version of ARIBA, the following commands can be used to install ARIBA and its dependencies. This was tested on a new instance of Ubuntu 16.04. sudo apt-get update sudo apt-get install -y python3-dev python3-pip python3-tk zlib1g-dev bowtie2 mummer cd-hit export ARIBA_CDHIT=cdhit-est sudo pip3 install ariba ### Dependencies and environment variables By default, ARIBA will look for the dependencies in your `$PATH`, using the names in the table below. This behaviour can be overridden and point ARIBA to a specific program using environment variables. The environment variable is checked first and is used if it is set. Otherwise ARIBA looks in your `$PATH` for the default name. This applies to the following dependencies. | Dependency | Default executable | Environment variable name | |----------------|------------------------|---------------------------| | Bowtie2 | `bowtie2` | `$ARIBA_BOWTIE2` | | CD-HIT (est) | `cd-hit-est` | `$ARIBA_CDHIT` | For example, you could specify an exact version of a bowtie2 executable that you compiled and downloaded in your home directory (assuming BASH): export ARIBA_BOWTIE2=$HOME/bowtie2-2.1.0/bowtie2 Note that ARIBA also runs `bowtie2-build`, for which it uses the `bowtie2` executable with `-build` appended. So in this case it would try to use $HOME/bowtie2-2.1.0/bowtie2-build ## Temporary files ARIBA can temporarily make a large number of files whilst running, which are put in a temporary directory made by ARIBA. The total size of these files is small, but there can be a many of them. This can be a problem when running large numbers (100s or 1000s) of jobs simultaneously on the same file system. The parent directory of the temporary directory is determined in the following order of precedence: 1. The value of the option `--tmp_dir` (if that option was used) 2. The environment variable `$ARIBA_TMPDIR` (if it is set) 3. The environment variable `$TMPDIR` (if it is set) 4. If none of the above is found, then use the run's output directory. Each temporary directory is unique to one run of ARIBA, and is automatically deleted at the end of the run (even if ARIBA was killed by the user or crashed). For example, export $ARIBA_TMPDIR=/tmp will result in the creation of a new directory inside `/tmp`, which will have a name of the form /tmp/ariba.tmp.abcdef where the suffix `abcdef` is a random string of characters, chosen such that `/tmp/ariba.tmp.abcdef` does not already exist. The exception to the above is if the option `--noclean` is used. This forces the temporary directory to be placed in the output directory, and temporary files are kept. It is intended for debugging. ## Usage usage: ariba <command> <options> optional arguments: -h, --help show this help message and exit Available commands: aln2meta Converts multi-aln fasta and SNPs to metadata expandflag Expands flag column of report file flag Translate the meaning of a flag getref Download reference data micplot Make violin/dot plots using MIC data prepareref Prepare reference data for input to "run" pubmlstget Download species from PubMLST and make db pubmlstspecies Get list of available species from PubMLST refquery Get cluster or sequence info from prepareref output run Run the local assembly pipeline summary Summarise multiple reports made by "run" test Run small built-in test dataset version Get versions and exit Please read the [ARIBA wiki page][ARIBA wiki] for full usage instructions. ## License ARIBA is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/ariba/blob/master/LICENSE). ## Feedback/Issues Please report any issues to the [issues page](https://github.com/sanger-pathogens/ariba/issues) or email ariba-help@sanger.ac.uk ## Citation If you use this software please cite: ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J , Keane JA, Harris SR. Microbial Genomics 2017. doi: [110.1099/mgen.0.000131](http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000131) [ariba biorxiv]: http://biorxiv.org/content/early/2017/04/07/118000 [bowtie2]: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml [cdhit]: http://weizhongli-lab.org/cd-hit/ [ARIBA wiki]: https://github.com/sanger-pathogens/ariba/wiki [mummer]: http://mummer.sourceforge.net/ [python]: https://www.python.org/ |
Commit History @upstream/2.12.1+ds
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- New upstream version 2.9.3+ds Sascha Steinbiss 7 years ago
- New upstream version 2.9.2+ds Sascha Steinbiss 7 years ago
- New upstream version 2.9.0+ds Sascha Steinbiss 7 years ago
- New upstream version 2.9.0+ds Sascha Steinbiss 7 years ago
- New upstream version 2.7.2+ds Sascha Steinbiss 7 years ago
- New upstream version 2.7.1+ds Sascha Steinbiss 7 years ago
- New upstream version 2.7.0+ds Sascha Steinbiss 7 years ago
- New upstream version 2.6.1+ds Sascha Steinbiss 7 years ago
- New upstream version 2.6.0+ds Sascha Steinbiss 7 years ago
- New upstream version 2.5.1+ds Sascha Steinbiss 7 years ago
- Merge branch 'upstream' of ssh://git.debian.org/git/debian-med/ariba into upstream Sascha Steinbiss 7 years ago
- New upstream version 2.5.0+ds Sascha Steinbiss 7 years ago
- New upstream version 2.4.0+ds Sascha Steinbiss 7 years ago
- New upstream version 2.3.0+ds Sascha Steinbiss 7 years ago
- Imported Upstream version 2.2.5+ds Sascha Steinbiss 7 years ago
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- Imported Upstream version 1.0.0 Sascha Steinbiss 7 years ago
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