staphb/fastani
staphb
StaPH-B docker-builds仓库提供集中化的Docker镜像资源，包含多种生物信息学工具的Dockerfile及构建文件，方便用户获取和使用，并提供详细的容器构建与使用文档。
2 次收藏下载次数: 0状态：社区镜像维护者：staphb仓库类型：镜像最近更新：2 年前
让 AI 帮你使用轩辕镜像？ · 展开查看说明 · 点击收起说明
如果你使用 DeepSeek、元宝 AI、Copilot、ChatGPT 等 AI 工具，协助配置轩辕镜像、编写 docker pull 命令、修改 Docker Compose 镜像地址、配置镜像加速、排查镜像拉取失败、分析报错日志等问题，请先让 AI 阅读并遵守轩辕镜像的规则文档。
只需在 AI 对话中先发送下面这句话即可：
请先完整阅读并严格遵守以下文档中的全部规则与要求：
https://xuanyuan.cloud/agents.md
在未充分阅读并理解该文档前，不要生成任何命令、配置、修改建议、故障排查方案或技术回答。后续所有输出都必须严格以该文档中的规范为最高优先级执行。查看 agents.md 用法指南与完整示范。国内用户首推 元宝 AI、DeepSeek 的深度思考模式，不推荐豆包 AI；Cursor 等编辑器可在对话 @ 该链接，或加入 User Rules。 若 AI 无法访问外链，可 打开说明文档 复制全文粘贴。文档会随站点更新，复制内容可能过期，建议定期检查。
StaPH-B docker-builds 镜像文档
镜像概述和主要用途
该仓库包含构建多种程序Docker镜像所需的Dockerfile和其他相关文件，这些程序供StaPH-B（州公共卫生实验室生物信息学）联盟成员使用。其目的是提供一个集中的Docker镜像位置，方便用户访问，并提供关于容器构建方式和使用方法的清晰文档。
核心功能和特性
- 集中化管理：提供多种生物信息学工具的Docker镜像，集中存储于Docker Hub的staphb仓库
- 详细文档：包含容器构建过程和使用方法的清晰说明
- 社区贡献：支持用户通过fork仓库、提交更改和Pull Request来贡献新镜像或改进现有镜像
- Singularity兼容性：大多数Docker容器可转换为Singularity格式，适用于无法使用Docker的环境
- 版本多样：每种工具提供多个版本，满足不同用户需求
使用场景和适用范围
适用于StaPH-B联盟成员及其他生物信息学研究人员，用于获取和运行各种生物信息学分析工具，如序列比对、变异检测、基因组组装、系统发育分析等。特别适合需要快速部署标准化生物信息学工具环境的场景。
贡献指南
如希望贡献Docker镜像或改进现有镜像，请fork仓库、进行更改/添加，然后提交Pull Request。如遇到现有镜像问题，请提交issue。欢迎所有反馈！
https://staph-b.github.io/docker-builds/contribute/
Docker用户指南
提供了使用和开发Docker容器的方法和最佳实践指南，详情请参见：https://staph-b.github.io/docker-builds/
Singularity兼容性
对于无法使用Docker的用户，Singularity是一个替代方案。大多数Docker容器与Singularity兼容，可以轻松转换为Singularity格式。有关如何从Docker Hub下载镜像并使用Singularity运行的说明，请参见上述用户指南。我们努力确保所有容器都与Singularity兼容，如发现不兼容情况，请提交issue反馈。
可用Docker镜像
https://travis-ci.com/StaPH-B/docker-builds.svg?branch=master](https://travis-ci.com/StaPH-B/docker-builds)%EF%BC%88%E6%9E%84%E5%BB%BA%E7%8A%B6%E6%80%81%E4%BB%85%E5%8F%8D%E6%98%A0%E5%B7%B2%E6%B7%BB%E5%8A%A0%E5%88%B0TravisCI%E6%B5%8B%E8%AF%95%E7%9A%84%E5%AE%B9%E5%99%A8%EF%BC%89
| 软件 | 版本 | 链接 |
|---|---|---|
| https://hub.docker.com/r/staphb/abricate/ https://img.shields.io/docker/pulls/staphb/abricate.svg?style=popout](https://hub.docker.com/r/staphb/abricate) |
| https://github.com/tseemann/abricate |
| https://hub.docker.com/r/staphb/ariba/ https://img.shields.io/docker/pulls/staphb/ariba.svg?style=popout](https://hub.docker.com/r/staphb/ariba) |
| https://github.com/sanger-pathogens/ariba |
| https://hub.docker.com/r/staphb/artic-ncov2019 https://img.shields.io/docker/pulls/staphb/artic-ncov2019?style=popout](https://hub.docker.com/r/staphb/artic-ncov2019) |
| https://github.com/artic-network/fieldbioinformatics |
| https://hub.docker.com/r/staphb/artic-ncov2019-medaka https://img.shields.io/docker/pulls/staphb/artic-ncov2019-medaka?style=popout](https://hub.docker.com/r/staphb/artic-ncov2019-medaka) |
| https://github.com/artic-network/artic-ncov2019 |
| https://hub.docker.com/r/staphb/artic-ncov2019-nanopolish https://img.shields.io/docker/pulls/staphb/artic-ncov2019-nanopolish?style=popout](https://hub.docker.com/r/staphb/artic-ncov2019-nanopolish) |
| https://github.com/artic-network/artic-ncov2019 |
| https://github.com/nextstrain/augur https://img.shields.io/docker/pulls/staphb/augur.svg?style=popout](https://hub.docker.com/r/staphb/augur) |
| https://github.com/nextstrain/augur |
| https://github.com/nextstrain/auspice https://img.shields.io/docker/pulls/staphb/auspice.svg?style=popout](https://hub.docker.com/r/staphb/auspice) |
| https://github.com/nextstrain/auspice |
| https://hub.docker.com/r/staphb/bbtools/ https://img.shields.io/docker/pulls/staphb/bbtools.svg?style=popout](https://hub.docker.com/r/staphb/bbtools) |
| https://jgi.doe.gov/data-and-tools/bbtools/ |
| https://hub.docker.com/r/staphb/bcftools/ https://img.shields.io/docker/pulls/staphb/bcftools.svg?style=popout](https://hub.docker.com/r/staphb/bcftools) |
| https://github.com/samtools/bcftools |
| https://hub.docker.com/r/staphb/bedtools/ https://img.shields.io/docker/pulls/staphb/bedtools.svg?style=popout](https://hub.docker.com/r/staphb/bedtools) |
| https://bedtools.readthedocs.io/en/latest/ https://github.com/arq5x/bedtools2 |
| https://hub.docker.com/r/staphb/bwa https://img.shields.io/docker/pulls/staphb/bwa.svg?style=popout](https://hub.docker.com/r/staphb/bwa) |
| https://github.com/lh3/bwa |
| https://hub.docker.com/r/staphb/canu https://img.shields.io/docker/pulls/staphb/canu.svg?style=popout](https://hub.docker.com/r/staphb/canu) |
| https://canu.readthedocs.io/en/latest/ https://github.com/marbl/canu |
| https://hub.docker.com/r/staphb/canu-racon/ https://img.shields.io/docker/pulls/staphb/canu-racon.svg?style=popout](https://hub.docker.com/r/staphb/canu-racon) |
| https://canu.readthedocs.io/en/latest/ https://github.com/lbcb-sci/racon https://github.com/isovic/racon (已归档) https://lh3.github.io/minimap2/ |
| https://hub.docker.com/r/staphb/centroid/ https://img.shields.io/docker/pulls/staphb/centroid.svg?style=popout](https://hub.docker.com/r/staphb/centroid) |
| https://github.com/stjacqrm/centroid |
| https://hub.docker.com/r/staphb/cdc-spn/ https://img.shields.io/docker/pulls/staphb/cdc-spn.svg?style=popout](https://hub.docker.com/r/staphb/cdc-spn) |
| https://github.com/BenJamesMetcalf/Spn_Scripts_Reference |
| https://hub.docker.com/r/staphb/cfsan-snp-pipeline https://img.shields.io/docker/pulls/staphb/cfsan-snp-pipeline.svg?style=popout](https://hub.docker.com/r/staphb/cfsan-snp-pipeline) |
| https://github.com/CFSAN-Biostatistics/snp-pipeline |
| https://hub.docker.com/r/staphb/circlator https://img.shields.io/docker/pulls/staphb/circlator.svg?style=popout](https://hub.docker.com/r/staphb/circlator) |
| https://github.com/sanger-pathogens/circlator |
| https://hub.docker.com/r/staphb/clustalo https://img.shields.io/docker/pulls/staphb/clustalo.svg?style=popout](https://hub.docker.com/r/staphb/clustalo) |
| http://www.clustal.org/omega/ |
| https://hub.docker.com/r/staphb/colorid https://img.shields.io/docker/pulls/staphb/colorid.svg?style=popout](https://hub.docker.com/r/staphb/colorid) |
| https://github.com/hcdenbakker/colorid |
| https://hub.docker.com/r/staphb/cutshaw-report-env https://img.shields.io/docker/pulls/staphb/cutshaw-report-env.svg?style=popout](https://hub.docker.com/r/staphb/cutshaw-report-env) |
| https://github.com/VADGS/CutShaw |
| https://hub.docker.com/r/staphb/emm-typing-tool https://img.shields.io/docker/pulls/staphb/emm-typing-tool.svg?style=popout](https://hub.docker.com/r/staphb/emm-typing-tool) |
| https://github.com/phe-bioinformatics/emm-typing-tool |
| https://hub.docker.com/r/staphb/fastani https://img.shields.io/docker/pulls/staphb/fastani.svg?style=popout](https://hub.docker.com/r/staphb/fastani) |
| https://github.com/ParBLiSS/FastANI |
| https://hub.docker.com/r/staphb/fasttree https://img.shields.io/docker/pulls/staphb/fasttree.svg?style=popout](https://hub.docker.com/r/staphb/fasttree) |
| http://www.microbesonline.org/fasttree/ |
| https://hub.docker.com/r/staphb/fastqc https://img.shields.io/docker/pulls/staphb/fastqc.svg?style=popout](https://hub.docker.com/r/staphb/fastqc) |
| https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ https://github.com/s-andrews/FastQC |
| https://hub.docker.com/r/staphb/filtlong https://img.shields.io/docker/pulls/staphb/filtlong.svg?style=popout](https://hub.docker.com/r/staphb/filtlong) |
| https://github.com/rrwick/filtlong |
| https://hub.docker.com/r/staphb/flye https://img.shields.io/docker/pulls/staphb/flye.svg?style=popout](https://hub.docker.com/r/staphb/flye) |
| https://github.com/fenderglass/Flye |
| https://hub.docker.com/r/staphb/hmmer https://img.shields.io/docker/pulls/staphb/hmmer.svg?style=popout](https://hub.docker.com/r/staphb/hmmer) |
| [***] |
| https://hub.docker.com/r/staphb/iqtree/ https://img.shields.io/docker/pulls/staphb/iqtree.svg?style=popout](https://hub.docker.com/r/staphb/iqtree) |
| http://www.iqtree.org/ |
| https://hub.docker.com/r/staphb/iqtree2/ https://img.shields.io/docker/pulls/staphb/iqtree2.svg?style=popout](https://hub.docker.com/r/staphb/iqtree2) |
| http://www.iqtree.org/ |
| https://hub.docker.com/r/staphb/ivar/ https://img.shields.io/docker/pulls/staphb/ivar.svg?style=popout](https://hub.docker.com/r/staphb/ivar) |
| https://github.com/andersen-lab/ivar |
| https://hub.docker.com/r/staphb/kma/ https://img.shields.io/docker/pulls/staphb/kma.svg?style=popout](https://hub.docker.com/r/staphb/kma) |
| https://bitbucket.org/genomicepidemiology/kma/ |
| https://hub.docker.com/r/staphb/kraken/ https://img.shields.io/docker/pulls/staphb/kraken.svg?style=popout](https://hub.docker.com/r/staphb/kraken) |
| https://github.com/DerrickWood/kraken |
镜像拉取方式
您可以使用以下命令拉取该镜像。请将 <标签> 替换为具体的标签版本。如需查看所有可用标签版本，请访问 标签列表页面。
DockerHub 原生拉取命令
docker pull staphb/fastani:<标签>
镜像拉取常见问题
功能
错误码
用户好评
来自真实用户的反馈，见证轩辕镜像的优质服务
oldzhang
运维工程师
Linux服务器
5
"Docker访问体验非常流畅，大镜像也能快速完成下载。"