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davelabhub/cloudconductor
自动构建
davelabhub
Cloud-based workflow manager that generates and executes bioinformatics pipelines.
下载次数: 0状态：自动构建维护者：davelabhub仓库类型：镜像最近更新：4 年前
CloudConductor: Simplified Bioinformatics
CloudConductor is a cloud-based workflow engine for defining and executing bioinformatics pipelines in a cloud environment. Currently, the framework has been tested extensively on the Google Cloud Platform, but will eventually support other platforms including AWS, Azure, etc.
Feature Highlights
- User-friendly
- Define complex workflows by linking together user-defined modules that can be re-used across pipelines
- Config_obj for clean, readable workflows (see below example)
- 50+ pre-installed modules for existing bioinformatics tools
- Portable
- Docker integration ensures reproducible runtime environment for modules
- Platform independent (currently supports GCP; AWS, Azure to come)
- Modular/Extensible
- Plug-N-Play with user-defined task modules
- Easily re-use, re-combine across workflows
- Eliminates serial copy/paste
- Easily add or customize task modules as needed
- Pre-Launch Type-Checking
- Strongly-typed task modules
- Catch pipeline errors prior to runtime
- Pre-launch validation ensures pipeline success/failure
- Strongly-typed task modules
- Scalable
- Removes resource limitations imposed by cluster-based HPCCs
- Elastic
- VM usage automatically scales to match input file sizes, computational needs
- Scatter-Gather Parallelism
- In-built logic for dividing large tasks into small chunks and re-combining
- Economical
- Preemptible/Spot instances drastically cut workflow costs
Setting up your system
CloudConductor is currently designed only for Linux systems. You will need to install and configure the following tools to run your pipelines on Google Cloud:
-
Python v3.6+
You can check your Python version by running the following command in your terminal:
sh$ python3 -V Python 3.6.8To install the correct version of Python, visit the official Python website.
-
Python packages: configobj, jsonschema, requests
You will need pip to install the above packages. After installing pip, run the following commands in your terminal:
sh# Upgrade pip sudo pip3 install -U pip # Install Python modules sudo pip3 install -U configobj jsonschema requests -
Clone the CloudConductor repo
sh# clone the repo git clone https://github.com/labdave/CloudConductor.git -
Google Cloud Platform SDK
Follow the instructions on the official Google Cloud website.
Documentation
Get started with our full documentation to explore the ways CloudConductor can streamline the development and execution of complex, multi-sample workflows typical in bioinformatics.
Project Status
CloudConductor is actively under development. To get involved or request features, please contact https://github.com/ripanea.
Authors & Contributors
- https://github.com/ripanea
- https://github.com/alexwaldrop
- https://github.com/tushardave26
- https://github.com/parkerc71
- https://github.com/qiuosier
- https://github.com/rkositsky
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。
轩辕镜像加速拉取命令点我查看更多 cloudconductor 镜像标签
docker pull docker.xuanyuan.run/davelabhub/cloudconductor:<标签>
DockerHub 原生拉取命令
docker pull davelabhub/cloudconductor:<标签>
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