GITO, a lightweight and safe container docker image based on Alpine containing bioinformatics tools ready to be used. The base image is only 4.41 MB in size and contains only the OS libraries and language de-pendencies required to run an application, but robust enough to run bioinformatics pipeline with security.
GITO is an open source using the Docker platform and provides an easy and modular method for building, distributing, and replicating pipelines, which has a base image (GITO-base) that forms the single foundation layer on which each container application is built. GITO was conceived with the "start with the minimum and add dependencies as needed" philosophy in mind, which have separate containers for each bioinformatics tool with the minimum to run. GITO use musl as the standard C library for Linux-based systems, called musl-libc. Musl-libc is free, lightweight, security-oriented and smaller in size compared to the Glibc library. The source code for bioinformatics tools, written in C, C ++ and Java, has been compiled for native Alpine executables.
To 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
The image can be downloaded and executed through the Docker's CLI with the following commands:
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Pull(download) the Docker images:
$ docker pull gitobioinformatics/fastqc$ docker pull gitobioinformatics/trimmomatic$ docker pull gitobioinformatics/trinity$ docker pull gitobioinformatics/bowtie2 -
Change the working directory to a project, and run the following commands:
Run FastQC
$ docker run -v $PWD:$PWD --rm gitobioinformatics/fastqcRun Trimmomatic
$ docker run -v $PWD:$PWD --rm gitobioinformatics/trimmomaticRun Trinity
$ docker run -v $PWD:$PWD --rm gitobioinformatics/trinityRun Bowtie2
$ docker run -v $PWD:$PWD --rm gitobioinformatics/bowtie2
You 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.
GITO was used to reproduce the pipeline present in the work of Hernández-Fernández (2017), which is the first de novo transcriptome assembly of Eretmochelys imbricate published(https://doi.org/10.1016/j.dib.2017.10.015), instructions used and execution results can be accessed here.
To build GITO images from source, you can use the following process:
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Install latest version of Docker
For Linux users, you can follow the instructions here to manage Docker as non-root user. Otherwise, execute
gitobldscript usingsudo. -
Get the source code.
$ git clone https://github.com/gitobioinformatics/gito.git $ cd gito -
Create a private and public key to sign the apk packages:
$ mkdir -p keys $ openssl genrsa -out keys/packager_key.rsa 2048 $ openssl rsa -in keys/packager_key.rsa -pubout -out keys/packager_key.rsa.pub -
Run the helper script to build the images:
$ ./gitobld build -SR allYou can build individual images by using the tool name instead of all.
| Directory | Description |
|---|---|
| base | Contains Dockerfile used to build GITO base image. |
| build | Utilities to create Docker images using GITO as base. |
| examples | Contains example of bioinformatics pipelines using GITO images. |
| library | Dockerfiles used to build several tools, using Alpine packages from ports directory. |
| ports | Contains APKBUILD files for bioinformatic tools. |
Due to the extremely small size, the GITO has a smaller attack surface compared to the containers that use larger images. To assess safety, we used Quay Security Scanner to assess vulnerabilities in the GITO. Quay identifies insecure packages by matching the metadata against Common Vulnerabilities and Exposures (CVE) vulnerability database. The results of the analysis were published in the Quay portal, and the scanning of each tool can be accessed below:
| Image | Scanning Result |
|---|---|
| Bowtie2 |  |
| FastQC | |
| Jellyfish | |
| Salmon | |
| Samtools | |
| SRA Tools | |
| Trimmomatic | |
| Trinity | |
MIT License. See LICENSE for more information
GITO is open-source (see LICENSE), and we welcome contributions from anyone who is interested in contributing. To contribute code, please make a pull request on github. The issue tracker for GITO is also available on github.
See CONTRIBUTING.md for more information.
The word "gito" is used by populations of the North of Brazil when people refer to something "very small, smaller than normal". The logo of the project was inspired by the Boto Tucuxi (Sotalia fluviatilis), which is one of the smallest dolphins in the Delphinidae family and the only one of this family that lives in rivers. It is a very agile dolphin, although it is an endangered species, it is still possible to find it in the rivers of the Amazon jumping in the air.
We thank the following institutions, which contributed to ensuring the success of our work:
Ministério da Ciência, Tecnologia, Inovação e Comunicação (MCTIC)
Museu Paraense Emílio Goeldi (MPEG)
Centro Universitário do Estado do Pará (CESUPA)
This work has been supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq (grants 149985/2018-5; 129954/2018-7)
Marcos Paulo Alves de Sousa
Franklin Gonçalves Sobrinho
Lucas Peres Oliveira
Kayke Correa Conceição Lins Pereira
Dr. Marcos Paulo Alves de Sousa (Project leader)
Email: [email protected]
Laboratório de Biologia Molecular
Museu Paraense Emílio Goeldi
Av. Perimetral 1901. CEP 66077- 530. Belém, Pará, Brazil.