[{"_1":2,"_176":-5,"_177":-5},"loaderData",{"_3":4,"_13":14,"_21":22,"_155":156},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","routes/_layout",{"_15":-5,"_16":17,"_18":17,"_19":11,"_20":11},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_23":24,"_25":-5,"_26":11,"_27":11,"_28":29,"_30":31,"_32":-5,"_33":11,"_34":35,"_84":85,"_108":109,"_146":-5,"_147":11,"_148":17,"_149":11,"_150":-5,"_151":11,"_152":-5,"_153":154},"canonicalUrl","https://hub.docker.com/r/sangerpathogens/companion/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","sangerpathogens","reponame","companion","cloudBuildSource","isAutobuildsAvailable","repo",{"_36":37,"_38":39,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":51,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":58,"_60":61,"_62":-5,"_63":64,"_65":66,"_67":11,"_68":29,"_69":70,"_75":17,"_76":77,"_81":29,"_82":83},"categories",[],"content_types",[40],"image","date_registered","2016-06-06T10:46:19.266179Z","description","Docker container for Companion's Nextflow pipeline","is_private","last_updated","2018-12-06T11:54:44.032866Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[52],"application/vnd.docker.container.image.v1+json","name","pull_count",1920,"repository_type","star_count",1,"status","status_description","active","source","collaborator_count",0,"full_description","# Companion\nA portable, scalable eukaryotic genome annotation pipeline implemented in Nextflow.\n\n[![Build Status](https://travis-ci.org/sanger-pathogens/companion.svg?branch=master)](https://travis-ci.org/sanger-pathogens/companion) \n[![License: ISC](https://img.shields.io/badge/License-ISC-brightgreen.svg)](https://github.com/sanger-pathogens/companion/blob/master/LICENSE) \n[![status](https://img.shields.io/badge/NAR-10.1093%2Fnar.gkw292-brightgreen.svg)](https://doi.org/10.1093/nar/gkw292)\n\nThis software is a comprehensive computational pipeline for the annotation of eukaryotic genomes (like protozoan parasites). It performs the following tasks:\n\n - Fast generation of pseudomolecules from scaffolds by ordering and orientating against a reference\n - Accurate transfer of highly conserved gene models from the reference\n - _De novo_ gene finding as a complement to the gene transfer\n - Non-coding RNA detection (tRNA, rRNA, sn(o)RNA, ...)\n - Pseudogene detection\n - Functional annotation (GO, products, ...)\n - ...by transferring reference annotations to the target genome\n - ...by inferring GO terms and products from Pfam pHMM matches\n - Consistent gene ID assignment\n - Preparation of validated GFF3, GAF and EMBL output files for jump-starting manual curation and quick turnaround time to submission\n\nIt supports parallelized execution on a single machine as well as on large cluster platforms (LSF, SGE, ...).\n\n\n## Contents\n\n * [Quick start](#quick-start)\n * [1. Install dependencies](#1-install-dependencies)\n * [2. Install Companion](#2-install-companion)\n * [3. Run Companion test job](#3-run-companion-test-job)\n * [4. Configure Companion for your annotation run](#4-configure-companion-for-your-annotation-run)\n * [5. Prepare reference annotations](#5-prepare-reference-annotations)\n * [6. Run it!](#6-run-it)\n * [Further technical information](#further-technical-information)\n * [Dependencies](#dependencies)\n * [Java](#java)\n * [Nextflow](#nextflow)\n * [Docker](#docker)\n * [Installation](#installation)\n * [Usage](#usage)\n * [Local copy of Companion](#local-copy-of-companion)\n * [Running Companion direct from a repository](#running-companion-direct-from-a-repository)\n * [Preparing reference annotations](#preparing-reference-annotations)\n * [License](#license)\n * [Feedback/Issues](#feedbackissues)\n * [Citation](#citation)\n\n## Quick start\n\nThis should get you up & running on an Ubuntu system, but please read the full documentation before before doing any work \"for real\".\n\n### 1. Install dependencies\n\nExecute these commands as root, e.g. using `sudo`\n```\napt-get install default-jre\ncurl -fsSL get.nextflow.io | bash && \\\n mv nextflow /usr/local/bin\ncurl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - && \\\n add-apt-repository \"deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable\" && \\\n apt-get update && \\\n apt-cache policy docker-ce && \\\n apt-get install --yes docker-ce && \\\n systemctl enable docker\n```\n\nTo enable you to use docker with your normal user account (i.e. without being root or needing to use sudo),\nrun the following command, with your username in place of ``.\n```\nusermod -aG docker \n```\nLog out and log back in again for this to take effect.\n\n#### Checks\n\n - `java -version` should say you have Java 1.8 or greater\n - `nextflow info` will print system information if nextflow has been installed successfully\n - `systemctl status docker` will tell you if docker is active (running)\n - `docker info` will print information if docker has been installed successfully, and you have permission to use it\n\n### 2. Install _Companion_\n\nExecute these commands in the directory you want to keep your _Companion_ work in. Do this as a normal user, i.e. not as root or using sudo.\nUse a name that is meaningful to you in place of ``\n```\ncurl -L -o companion-master.zip https://github.com/sanger-pathogens/companion/archive/master.zip && \\\n unzip companion-master.zip && \\\n mv companion \ndocker pull sangerpathogens/companion\n```\n\n### 3. Run _Companion_ test job\n\n_Companion_ is distributed with configuration and data (including a few pregenerated reference annotations) for a small test run. Run\nthe following command (using the name you chose for your project directory in place of `my-companion-project`).\n```\nnextflow run my-companion-project -profile docker\n```\nThis will create a directory `my-companion-project/example-output` with the results of the run.\n\n### 4. Configure _Companion_ for your annotation run\n\nThe file `params_default.config` configures the pipeline, and will need to be edited for your annotation run. You will probably need to change at least the following parameters:\n\n*inseq* Your input FASTA file (`${baseDir}/example-data/L_donovani.1.fasta` in the example parameter file included wirth the distribution)\n\n*ref_dir* The directory containing your reference genomes (`${baseDir}/example-data/references` in the example file)\n\n*ref_species* The \"short name\" for your reference species (`LmjF.1` in the example file)\n\n*dist_dir* The directory that will contain the newly created output files (`${baseDir}/example-data-output` in the example file)\n\n*GENOME_PREFIX* Text pattern matching your genome prefix (`LDON` in the example file)\n\n*CHR_PATTERN* Pattern matching your chromosome names (`LDON_(%w+)` in the example file, where `%w+` matches one or more letters or numbers)\n\n*ABACAS_BIN_CHR* Abacas bin chromosome (`LDON_0` in the example file)\n\n*EMBL_AUTHORS* etc.; please provide suitable EMBL metadata (dummy values in the example file)\n\n*TAXON_ID* Please provide suitable value for the GAF output (`4711` in the example file)\n\n### 5. Prepare reference annotations\n\nThe reference annotations used in the pipeline need to be pre-processed before they can be used. To add a reference organism, you will need:\n\n- a descriptive name of the organism\n- a short abbreviation for the organism\n- the genome sequence in a single FASTA file\n- a structural gene annotation in GFF3 format (see below for details)\n- functional GO annotation in GAF 1.0 format, on the gene level\n- a pattern matching chromosome headers, describing how to extract chromosome numbers from them\n- an [AUGUSTUS](http://bioinf.uni-greifswald.de/augustus/) model, trained on reference genes\n\nInsert these file names, etc., where `` appear in the steps below:\n\n1. Create a new data directory (i.e. the equivalent of the `example-data` directory included in the distribution)\n1. Edit `nextflow.config` (and any config files that are referenced) and change parameters such as\n`inseq` and `ref_dir` to your new data directory.\n1. Copy the new reference genome (FASTA) into `/genomes`\n1. Copy GFF3 and GAF files into `/genomes`\n1. Copy Augustus model files into `data/augustus/species//`\n1. Create new directory `/references//`\n1. Add new section to `/references/references-in.json`, using the\nshort name (same as the directory name in the previous step); in this section add\nthe names/paths of the files copied (above), a descriptive name, and\na pattern for matching chromosomes in the FASTA files (in this example, _, where _n_ in any integer).\n```\n\"\" : { \"gff\" : \"../genomes/.gff3\",\n \"genome\" : \"../genomes/.fasta\",\n \"gaf\" : \"../genomes/.gaf\",\n \"name\" : \"\",\n \"augustus_model\" : \"../../data/augustus/species//\",\n \"chromosome_pattern\" : \"_(%d+)\"\n }\n```\n8. Finally, change directory to `/references` (you _must_ execute the following command in this directory)\nand run `../../bin/update_references.lua`. This writes the file `/references/references.json`.\n\n### 6. Run it!\n\nThe following command (using the name you chose for your project directory in place of `my-companion-project`) will\nstart your annotation run:\n```\nnextflow run my-companion-project -profile docker\n```\n\n\n## Further technical information\n\n### Dependencies\n\nCompanion has the following dependencies:\n\n - [Java](https://openjdk.java.net/) 8 or later\n - [Nextflow](http://nextflow.io)\n - [Docker](https://www.docker.com/) (if using the Docker image to satisfy dependencies)\n\n#### Java\n\nTo check if you have Java installed, and the version, use the command `java -version`. Note that this will give you a version number\nof 1.8 for Java 8, 1.9 for Java 9, etc.\n\nTo install Java 8 on an Ubuntu or Debian system, run:\n```\napt-get install openjdk-8-jre\n```\nOn Fedora, Centos or Red Hat (etc.) systems:\n```\nyum install java-1.8.0-openjdk\n```\n\n#### Nextflow\n\nTo install Nextflow, run:\n```\ncurl -fsSL get.nextflow.io | bash\n```\nThis will create an executable called 'nextflow', which should be moved to a suitable directory, for example:\n```\nmv nextflow /usr/local/bin/\n```\nUse the command `which nextflow` to check that it is found in your path.\n\n#### Docker\n\nDocker is required if you intended to use the Docker image, as recommended below, to satisfy the dependencies.\n\nTo install Docker, see the installation guide for\n[Ubuntu](https://docs.docker.com/install/linux/docker-ce/ubuntu/),\n[Centos](https://docs.docker.com/install/linux/docker-ce/centos/),\n[Debian](https://docs.docker.com/install/linux/docker-ce/debian/) or\n[Fedora](https://docs.docker.com/install/linux/docker-ce/fedora/).\n\nUsers running Companion with Docker will need to be added to the `docker` group (unix users can belong to one or more groups, which determine\nwhether they can peform certain actions; adding a user to the docker group allows them to execute docker commands). To add the user with\nusername ``, to the docker group, run:\n```\nusermod -aG docker \n```\n\n> _Some Linux systems may not have_ `usermod` _installed, as there are different programs that can be used to change user settings;_\n> _please consult your Linux distribution documentation if necessary._\n\n### Installation\n\nThere are a number of ways to install Companion; details for an installation using Docker are described below. If you encounter an issue when installing Companion please contact your local system administrator. If you encounter a bug please log it [here](https://github.com/sanger-pathogens/companion/issues) or email us at path-help@sanger.ac.uk.\n\nThe easiest way to use the pipeline is to use the prepared [Docker image](https://hub.docker.com/r/sangerpathogens/companion/) which contains all external dependencies.\n```\ndocker pull sangerpathogens/companion\n```\n\n### Usage\n\n#### Local copy of Companion\n\nTo create a local copy of companion, you can download this repo from github (if you are familiar with github, you may\nof course prefer to _clone_ or _fork_ it).\n```\ncurl -L -o companion-master.zip https://github.com/sanger-pathogens/companion/archive/master.zip # or click the green button on the guthub web page\nunzip companion-master.zip\nmv companion-master my-companion-project # renaming it to something meaningful to you is a good idea\n```\n\nNow you can run Companion. There is an example dataset and parameterization included in the distribution, so\nto get started just run:\n```\nnextflow run my-companion-project -profile docker\n```\nThe argument `-profile docker` instructs nextflow to run the sangerpathogens/companion docker image for the dependencies;\nthe `nextflow.config` file (and files referenced within it) define the docker profile and the docker image to be used.\n\n#### Running Companion direct from a repository\n\nIf you run nextflow with the name of a github repository, it will pull (download) the contents of the repository and run with those.\nFor example, the following command will do the same as the \"local copy\" example above:\n```\nnextflow run sanger-pathogens/companion -profile docker\n```\nIt is best to use this with some caution. After the command above is\nrun, nextflow will have stored a local copy of the repository in `.nextflow/assets/sanger-pathogens`\n(note that `.nextflow` is a hidden directory, and will not usually be visible; use the command `ls -la .nextflow` to see it).\n\nIf you run the same command again it will this time use the _local_ copy instead of pulling a copy from the repository. You can\nedit the files in your local copy, and nextflow will work from your (now different) version of sanger-pathogens/companion.\n\nIf you are familiar with repositories, and the workflow appropriate to using them, this can be a very convenient way of\nworking. You can create your own github repository to store and share your work, and track versions.\n\nIf you are not familiar with git repositories, it can become quite confusing, and you should probably work with a simple local copy.\n\n\n#### Preparing reference annotations\n\nFurther documentation on preparing reference data can be found in the\n[GitHub wiki](https://github.com/sanger-pathogens/companion/wiki/Preparing-reference-data-sets).\n\n\n## License\nCompanion is free software, licensed under [ISC](https://github.com/sanger-pathogens/companion/blob/master/LICENSE).\n\n## Feedback/Issues\nPlease report any issues to the [issues page](https://github.com/sanger-pathogens/companion/issues) or email path-help@sanger.ac.uk\n\n## Citation\nIf you use this software please cite:\n__Companion: a web server for annotation and analysis of parasite genomes.__\nSteinbiss S, Silva-Franco F, Brunk B, Foth B, Hertz-Fowler C et al.\nNucleic Acids Research, 44:W29-W34, 2016. \nDOI: [10.1093/nar/gkw292](http://dx.doi.org/10.1093/nar/gkw292)\n","has_starred","hub_user","immutable_tags_settings",{"_71":11,"_72":73},"enabled","rules",[74],".*","is_automated","permissions",{"_78":17,"_79":11,"_80":11},"read","write","admin","user","storage_size",36970072042,"orgData",{"_86":87,"_88":89,"_90":91,"_92":29,"_93":94,"_95":96,"_97":98,"_99":100,"_101":102,"_103":104,"_105":94,"_106":94,"_107":17},"id","54debe2b7cb846c08d04d8960295a6dc","uuid","54debe2b-7cb8-46c0-8d04-d8960295a6dc","type","organization","orgname","full_name","","location","Hinxton, UK","company","Wellcome Sanger Institute","profile_url","http://www.sanger.ac.uk/science/groups/pathogen-informatics","date_joined","2016-06-06T10:27:51.483834Z","gravatar_url","https://www.gravatar.com/avatar/99466499a237742acbff410e2328645e?s=80&r=g&d=mm","gravatar_email","badge","is_active","recentTags",[110],{"_111":40,"_112":113,"_114":115,"_86":116,"_117":118,"_46":135,"_136":113,"_137":29,"_138":52,"_53":139,"_140":141,"_142":126,"_143":135,"_144":61,"_145":17},"content_type","creator",884164,"full_size",1755364647,3302808,"images",[119],{"_120":121,"_122":123,"_124":94,"_125":126,"_127":128,"_129":130,"_131":94,"_132":-5,"_133":115,"_59":61,"_134":-5},"architecture","amd64","digest","sha256:234e4d8f4293985fe454ff242e746c877cd465718c7face19de7501f58bf2a36","features","last_pulled","2026-09-22T11:58:56.156355Z","last_pushed","2018-12-06T11:54:44Z","os","linux","os_features","os_version","size","variant","2018-12-06T11:54:43.652912Z","last_updater","last_updater_username","media_type","latest","repository",727677,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"routes/_layout.r.$namespace.$reponame.tags",{"_34":157,"_164":165,"_153":174,"_175":11},{"_36":158,"_38":159,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":160,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":58,"_60":61,"_62":-5,"_63":64,"_65":66,"_67":11,"_68":29,"_69":161,"_75":17,"_76":163,"_81":29,"_82":83},[],[40],[52],{"_71":11,"_72":162},[74],{"_78":17,"_79":11,"_80":11},"tags",{"_166":58,"_167":-5,"_168":-5,"_169":170},"count","next","previous","results",[171],{"_111":40,"_112":113,"_114":115,"_86":116,"_117":172,"_46":135,"_136":113,"_137":29,"_138":52,"_53":139,"_140":141,"_142":126,"_143":135,"_144":61,"_145":17},[173],{"_120":121,"_122":123,"_124":94,"_125":126,"_127":128,"_129":130,"_131":94,"_132":-5,"_133":115,"_59":61,"_134":-5},[],"canDeleteTags","actionData","errors"]

sangerpathogens/companion

Tags for sangerpathogens/companion