[{"_1":2,"_193":-5,"_194":-5},"loaderData",{"_3":4,"_18":19,"_25":26,"_168":169},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7,"_13":14,"_15":16,"_17":11},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","theme","system","contrast","normal","dockerRebrandTour","routes/_layout",{"_20":-5,"_21":22,"_23":11,"_24":22},"username","isAskGordonEnabled",true,"showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_27":28,"_29":-5,"_30":11,"_31":11,"_32":33,"_34":35,"_36":-5,"_37":11,"_38":39,"_88":89,"_110":111,"_156":-5,"_157":11,"_158":22,"_159":11,"_160":11,"_161":-5,"_162":11,"_163":-5,"_164":165,"_166":112,"_167":-7},"canonicalUrl","https://hub.docker.com/r/gitobioinformatics/gito/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","gitobioinformatics","reponame","gito","cloudBuildSource","isAutobuildsAvailable","repo",{"_40":41,"_42":43,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":55,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":62,"_69":70,"_71":11,"_72":33,"_73":74,"_79":11,"_80":81,"_85":33,"_86":87},"categories",[],"content_types",[44],"image","date_registered","2018-12-06T19:21:26.357097Z","description","Gito, a lightweight and safe environment for bioinformatics","is_private","last_updated","2019-10-16T17:01:33.764377Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[56],"application/vnd.docker.container.image.v1+json","name","pull_count",215,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","[![DOI](https://zenodo.org/badge/160723954.svg)](https://zenodo.org/badge/latestdoi/160723954)\n\n# Gito - A lightweight and safe environment for bioinformatics\n\n### Full Description:\n\nGito is a lightweight and safe Docker image based on Alpine containing bioinformatics tools ready to be used. It's an open source project that provides an easy and modular method for building, distributing and replicating pipelines, those of which hava a base image that forms the foundation layer on which each container is built. The base image is only 4.41 MB in size and contains only the OS libraries and language dependencies required to run the tools, but robust enough to run bioinformatics pipelines with security.\n\nGito was conceived with the \"start with the minimum and add dependencies as needed\" philosophy in mind, meaning we encourage separate containers for each bioinformatics tool configured with the minimum to run. Gito uses musl libc as the standard C library for Linux-based systems. Musl libc is free, lightweight, security-oriented and smaller in size compared to the Glibc library. The source codes for bioinformatics tools, written in C, C++ and Java, have been compiled for native Alpine executables.\n\n---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n\n### Guide to downloading and running this Docker image\n#### Step 1: Install Docker\n\nTo download and run this Docker image, you first need to set up Docker on your machine. The easiest way to start with Docker is to install the Docker Desktop (https://www.docker.com/products/docker-desktop) by simply downloading and clicking the installer which is available for both Mac OSX and Windows. For Linux users, follow the instructions here, and to use the CLI without sudo, follow the post-installation steps.\n \n#### Step 2: Download and run the Docker image\n\n1. Pull(download) the Docker images:\n \n ```\n $ docker pull gitobioinformatics/fastqc\n ```\n \n ```\n $ docker pull gitobioinformatics/trimmomatic\n ``` \n\n ```\n $ docker pull gitobioinformatics/trinity\n ``` \n\n ```\n $ docker pull gitobioinformatics/bowtie2\n ```\n\n2. Change the working directory to a project and run the following commands:\n \n - FastQC\n \n ```\n $ docker run -u $(id -u):$(id -g) -v $PWD:/data -w /data --rm gitobioinformatics/fastqc\n ```\n \n - Trimmomatic\n \n ```\n $ docker run -u $(id -u):$(id -g) -v $PWD:/data -w /data --rm gitobioinformatics/trimmomatic\n ```\n \n - Trinity\n \n ```\n $ docker run -u $(id -u):$(id -g) -v $PWD:/data -w /data --rm gitobioinformatics/trinity\n ```\n \n - Bowtie2\n \n ```\n $ docker run -u $(id -u):$(id -g) -v $PWD:/data -w /data --rm gitobioinformatics/bowtie2\n ```\n\n#### Deploy this Docker image onto your cloud\n\nYou can download and deploy this Docker image with your cloud provider such as DigitalOcean, Amazon Web Services, HP Enterprise, IBM, Microsoft Azure Cloud or others.\n\n---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n\n### Reproducing a pipeline example\n\nGito was used to reproduce the pipeline present in the work of [Hernández-Fernández (2017)](https://doi.org/10.1016/j.dib.2017.10.015), which is the first *de novo* transcriptome assembly of *Eretmochelys Imbricata* published. Instructions used and execution results can be [accessed here](https://github.com/gitobioinformatics/gito/tree/master/examples/eretmochelys_imbricata).\n\n---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n\n### Security and vulnerabilities\n\nDue to the extremely small size, Gito has a smaller attack surface compared to the containers that are based on larger images. To assess safety, we used [Quay Security Scanner](https://quay.io) to assess vulnerabilities in Gito. Quay identifies insecure packages by matching the metadata against Common Vulnerabilities and Exposures (CVE) database.\n\n---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n\n### License\n\nMIT License. See [LICENSE](https://github.com/gitobioinformatics/gito/blob/master/LICENSE) for more information\n\n---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n\n### Contributions\n\nGito is open-source (see [LICENSE](https://github.com/gitobioinformatics/gito/blob/master/LICENSE)), and we welcome contributions from anyone who is interested in contributing. To contribute, please make a pull request on GitHub. The issue tracker for Gito is also available on GitHub.\n\n---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n\n### Inspirations\n\nThe word \"gito\" is used by people from the North of Brazil when they refer to something \"very small, smaller than normal\".\nThe logo of the project was inspired by the tucuxi (*Sotalia fluviatilis*), which is one of the smallest dolphins of the Delphinidae family and the only one of this family that lives in the rivers. It is a very agile dolphin and although it is an endangered species, it is still possible to find it in Amazonian rivers jumping in the air.\n\n---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n\n### Acknowledgements\n\nWe thank the following institutions, which contributed to ensuring the success of our work:\n\nMinistério da Ciência, Tecnologia, Inovação e Comunicação (MCTIC)\n \nMuseu Paraense Emílio Goeldi (MPEG)\n \nCentro Universitário do Estado do Pará (CESUPA)\n\n---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n\n### Funding\n\nThis work has been supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq (grants 149985/2018-5; 129954/2018-7).\n\n---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n\n### Authors\n\n Marcos Paulo Alves de Sousa
\n Franklin Gonçalves Sobrinho
\n Lucas Peres Oliveira
\n Kayke Correa Conceição Lins Pereira\n \n ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n\n ### Contact\n\n Dr. Marcos Paulo Alves de Sousa (Project leader)\n \n Email: msousa@museu-goeldi.br
\n Laboratório de Biologia Molecular
\n Museu Paraense Emílio Goeldi
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gitobioinformatics/gito

Tags for gitobioinformatics/gito