GitHub Issues Statistics
13 |├── contributors.txt ├── create_cname.sh ├── config ├── prod.env.js ├── dev.env.js └── index.js ├── src ├── assets │ ├── logo.png │ └── iviewtheme │ │ ├── fonts │ │ ├── ionicons.ttf │ │ └── ionicons.woff │ │ └── index.less ├── store │ └── store.js ├── App.vue ├── router │ └── index.js ├── components │ ├── VulnerabilitiesModal.vue │ ├── Nav.vue │ ├── charts │ │ └── Heatmap.vue │ ├── NotFound.vue │ ├── Mappingdata.vue │ ├── Multipackage.vue │ ├── Index.vue │ ├── Registry.vue │ └── Tool.vue └── main.js ├── static ├── images │ ├── cwl.png │ ├── conda.png │ ├── cwl-2.png │ ├── docker.png │ ├── elixir.png │ ├── ga4gh.png │ ├── galaxy.png │ ├── bioconda.png │ ├── container.png │ ├── nextflow.png │ ├── workflow.jpg │ ├── workflow.png │ ├── bioconda-2.png │ ├── container-2.png │ ├── container-3.png │ ├── containers.png │ ├── singularity.png │ ├── source-code.jpg │ ├── source-code.png │ ├── workflow-2.png │ └── source-code-2.png ├── repodata │ ├── repodata.json.gz │ ├── bioconda │ │ ├── .DS_Store │ │ └── repodata.json.gz │ ├── condaforge │ │ ├── .DS_Store │ │ └── repodata.json.gz │ └── anaconda │ │ └── repodata.json.gz ├── logo │ └── biocontainers-logo.png └── font │ └── iconfont.js ├── .gitignore ├── .travis.yml ├── Dockerfile ├── nginx.conf ├── 404.html ├── .github └── workflows │ └── build.yml ├── README.md ├── index.html ├── package.json └── LICENSE /contributors.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /create_cname.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | echo 'biocontainers.pro' > ./dist/CNAME -------------------------------------------------------------------------------- /config/prod.env.js: -------------------------------------------------------------------------------- 1 | 'use strict' 2 | module.exports = { 3 | NODE_ENV: '"production"' 4 | } 5 | -------------------------------------------------------------------------------- /src/assets/logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/src/assets/logo.png -------------------------------------------------------------------------------- /static/images/cwl.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/cwl.png -------------------------------------------------------------------------------- /static/images/conda.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/conda.png -------------------------------------------------------------------------------- /static/images/cwl-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/cwl-2.png -------------------------------------------------------------------------------- /static/images/docker.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/docker.png -------------------------------------------------------------------------------- /static/images/elixir.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/elixir.png -------------------------------------------------------------------------------- /static/images/ga4gh.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/ga4gh.png -------------------------------------------------------------------------------- /static/images/galaxy.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/galaxy.png -------------------------------------------------------------------------------- /static/images/bioconda.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/bioconda.png -------------------------------------------------------------------------------- /static/images/container.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/container.png -------------------------------------------------------------------------------- /static/images/nextflow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/nextflow.png -------------------------------------------------------------------------------- /static/images/workflow.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/workflow.jpg -------------------------------------------------------------------------------- /static/images/workflow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/workflow.png -------------------------------------------------------------------------------- /static/images/bioconda-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/bioconda-2.png -------------------------------------------------------------------------------- /static/images/container-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/container-2.png -------------------------------------------------------------------------------- /static/images/container-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/container-3.png -------------------------------------------------------------------------------- /static/images/containers.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/containers.png -------------------------------------------------------------------------------- /static/images/singularity.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/singularity.png -------------------------------------------------------------------------------- /static/images/source-code.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/source-code.jpg -------------------------------------------------------------------------------- /static/images/source-code.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/source-code.png -------------------------------------------------------------------------------- /static/images/workflow-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/workflow-2.png -------------------------------------------------------------------------------- /static/images/source-code-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/images/source-code-2.png -------------------------------------------------------------------------------- /static/repodata/repodata.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/repodata/repodata.json.gz -------------------------------------------------------------------------------- /static/logo/biocontainers-logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/logo/biocontainers-logo.png -------------------------------------------------------------------------------- /static/repodata/bioconda/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/repodata/bioconda/.DS_Store -------------------------------------------------------------------------------- /static/repodata/condaforge/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/repodata/condaforge/.DS_Store -------------------------------------------------------------------------------- /src/assets/iviewtheme/fonts/ionicons.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/src/assets/iviewtheme/fonts/ionicons.ttf -------------------------------------------------------------------------------- /src/assets/iviewtheme/fonts/ionicons.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/src/assets/iviewtheme/fonts/ionicons.woff -------------------------------------------------------------------------------- /static/repodata/anaconda/repodata.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/repodata/anaconda/repodata.json.gz -------------------------------------------------------------------------------- /static/repodata/bioconda/repodata.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/repodata/bioconda/repodata.json.gz -------------------------------------------------------------------------------- /static/repodata/condaforge/repodata.json.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioContainers/registry/HEAD/static/repodata/condaforge/repodata.json.gz -------------------------------------------------------------------------------- /src/assets/iviewtheme/index.less: -------------------------------------------------------------------------------- 1 | @import '~iview/src/styles/index.less'; 2 | 3 | // Here are the variables to cover, such as: 4 | @primary-color: #f79321; -------------------------------------------------------------------------------- /config/dev.env.js: -------------------------------------------------------------------------------- 1 | 'use strict' 2 | const merge = require('webpack-merge') 3 | const prodEnv = require('./prod.env') 4 | 5 | module.exports = merge(prodEnv, { 6 | NODE_ENV: '"development"' 7 | }) 8 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Created by .ignore support plugin (hsz.mobi) 2 | ### Example user template template 3 | ### Example user template 4 | 5 | # IntelliJ project files 6 | .idea 7 | *.iml 8 | out 9 | gen 10 | dist/ 11 | node_modules/ 12 | 13 | -------------------------------------------------------------------------------- /src/store/store.js: -------------------------------------------------------------------------------- 1 | import Vue from 'vue'; 2 | import Vuex from 'vuex'; 3 | 4 | //只要是plugin,都可以用这种use的方法去应用。 5 | Vue.use(Vuex); 6 | 7 | export default new Vuex.Store({ 8 | state:{ 9 | baseURL: location.hostname.match(/localhost/)?'':'', 10 | //baseApiURL: location.hostname.match(/localhost/)?'http://localhost':'http://api.biocontainers.pro', 11 | baseApiURL: 'https://api.biocontainers.pro/', 12 | }, 13 | }); -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: node_js 2 | node_js: 3 | - "9" 4 | dist: trusty 5 | sudo: false 6 | 7 | branches: 8 | only: 9 | - master 10 | 11 | cache: 12 | directories: 13 | - node_modules 14 | 15 | install: 16 | - npm install 17 | 18 | script: 19 | - npm run build 20 | - echo 'Build happen' 21 | - bash ./create_cname.sh 22 | - echo 'CNAME created' 23 | 24 | deploy: 25 | provider: pages 26 | skip_cleanup: true 27 | github_token: $GITHUB_TOKEN 28 | local_dir: dist 29 | on: 30 | branch: master -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- 1 | FROM node:12.13.0-alpine as build-stage 2 | 3 | # Create app directory 4 | WORKDIR /app 5 | 6 | # Install app dependencies 7 | # A wildcard is used to ensure both package.json AND package-lock.json are copied 8 | # where available (npm@5+) 9 | COPY package*.json nginx.conf ./ 10 | 11 | RUN npm install 12 | COPY . ./ 13 | RUN npm run build 14 | 15 | FROM nginx:1.17.6 16 | COPY --from=build-stage /app/dist/ /etc/nginx/html/ 17 | # Copy the default nginx.conf provided by tiangolo/node-frontend 18 | COPY --from=build-stage /app/nginx.conf /etc/nginx/nginx.conf 19 | RUN apt-get update && apt-get install -y curl && apt-get install -y iputils-ping 20 | -------------------------------------------------------------------------------- /nginx.conf: -------------------------------------------------------------------------------- 1 | worker_processes 1; 2 | pid /tmp/nginx.pid; 3 | events { 4 | worker_connections 1024; 5 | } 6 | 7 | http { 8 | include /etc/nginx/mime.types; 9 | default_type application/octet-stream; 10 | access_log /tmp/access.log; 11 | sendfile on; 12 | keepalive_timeout 65; 13 | server { 14 | listen 8080; 15 | server_name localhost; 16 | location ~ / { 17 | gzip on; 18 | gzip_types text/plain application/xml text/javascript application/javascript application/x-javascript text/css application/json application/octet-stream image/jpeg image/png image/gif; 19 | try_files $uri $uri/ /index.html; 20 | } 21 | } 22 | } 23 | 24 | -------------------------------------------------------------------------------- /404.html: -------------------------------------------------------------------------------- 1 | 2 | 3 |
4 | 11 | 12 | 13 | -------------------------------------------------------------------------------- /.github/workflows/build.yml: -------------------------------------------------------------------------------- 1 | # This workflow will do a clean install of node dependencies, cache/restore them, build the source code and run tests across different versions of node 2 | # For more information see: https://help.github.com/actions/language-and-framework-guides/using-nodejs-with-github-actions 3 | 4 | name: Build 5 | 6 | on: 7 | push: 8 | branches: [ master ] 9 | pull_request: 10 | branches: [ master ] 11 | 12 | jobs: 13 | deploy: 14 | runs-on: ubuntu-latest 15 | steps: 16 | - name: Checkout 🛎️ 17 | uses: actions/checkout@v2.3.1 18 | 19 | - name: Install and Build 🔧 # This example project is built using npm and outputs the result to the 'build' folder. Replace with the commands required to build your project, or remove this step entirely if your site is pre-built. 20 | run: | 21 | npm install 22 | npm run build 23 | bash ./create_cname.sh 24 | echo 'CNAME created' 25 | 26 | - name: Deploy 🚀 27 | uses: JamesIves/github-pages-deploy-action@4.1.5 28 | with: 29 | branch: gh-pages 30 | folder: dist 31 | clean: true 32 | 33 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | BioContainers Web 2 | ============================== 3 | [](https://travis-ci.org/BioContainers/registry) 4 | 5 | 6 | This project contains the [main page of biocontainers](https://biocontainers.pro) and the [registry page](https://biocontainers.pro/registry). 7 | 8 | 9 | BioContainers Tool Registry 10 | --------------------------------- 11 | 12 | This project provides a web UI for [BioContainers](https://biocontainers.pro) 13 | 14 | * This application is written in JavaScript, and you can deploy this application easily. 15 | * This application doesn't store any user data. 16 | * You can find the necessary information simply from the Docker Registry [documentation](http://biocontainers.pro/docs/101/biocontainers-registry/). 17 | 18 | 19 | How to Test 20 | ------------------------ 21 | 22 | - Run the following installing command: 23 | 24 | ``` 25 | npm install 26 | ``` 27 | 28 | - Run the command: 29 | 30 | ``` 31 | npm run dev 32 | ``` 33 | 34 | Contributing 35 | -------------------- 36 | 37 | Please for the master branch, create a PR and after accepting the PR your changes will be seen in http://biocontainers.pro 38 | -------------------------------------------------------------------------------- /src/App.vue: -------------------------------------------------------------------------------- 1 | 2 |File not found
6 | 7 |8 | The site configured at this address does not 9 | contain the requested file. 10 |
11 | 12 |
13 | If this is your site, make sure that the filename case matches the URL.
14 | For root URLs (like http://example.com/) you must provide an
15 | index.html file.
16 |
19 | Read the full documentation 20 | for more information about using GitHub Pages. 21 |
22 | 23 |GitHub Issues Statistics
13 |Packages
13 |Selected Packages
28 |To create a container, please add the following string to this file as a pull request:
35 |Container name:
39 |
7 |
8 | BioContainers Flow
37 |SOFTWARE
40 |
41 |
42 | CONTAINER
47 |
48 |
49 | WORKFLOW
54 |
55 |
56 | Main Components
64 |Registry
68 |List of bioinformatics containers and workflows including metadata, statistics
69 | Registry 70 |Specifications
75 |Specifications, and architecture to create, deploy and maintain software containers using Conda and 76 | Docker technologies
77 | Read More 78 |Resources
83 |We provide multiple tools and resources to work with containers
84 | Multi-tools 85 | TRS API 86 |Partners
96 |
101 |
102 |
103 |
107 |
108 |
109 |
110 |
114 |
115 |
116 |
122 |
123 |
124 |
127 |
128 |
129 |
132 |
133 |
134 | Documentation
155 |How to create a containers, how to use it into a workflow, everything you need to 156 | know about BioContainers
157 | Documentation 158 |How to Cite
164 |da Veiga Leprevost F, Grüning BA, .. Perez-Riverol Y. Bioinformatics. 2017 165 | Aug 15;33(16):2580-2582. BioContainers: 166 | an open-source and community-driven framework for software standardization
167 |
67 |
68 |
69 |
149 |
150 |