Simplifying genomics workflows in the cloud!
+**The Amazon Genomics CLI project has entered its End Of Life (EOL) phase**. The code is no longer actively maintained and the **Github repository will be archived on May 31 2024**. During this time, we encourage customers to migrate to [AWS HealthOmics](https://aws.amazon.com/healthomics/) to run their genomics workflows on AWS, or [reach out to their AWS account team](https://aws.amazon.com/contact-us/?nc2=h_header) for alternative solutions. While the source code of AGC will still be available after the EOL date, we will not make any updates inclusive of addressing issues or accepting Pull Requests. {{< blocks/link-down color="info" >}} {{< /blocks/cover >}} {{% blocks/lead color="primary" %}} -Amazon Genomics CLI is an **open source CLI** that helps customers run genomics workflows in the cloud by **automating deployment of best practices infrastructure** for workflow engines. Amazon Genomics CLI reduces the time for scientists and developers to start running existing genomics workflows at scale and speed up iteration cycles as they develop new ones. -{{% /blocks/lead %}} - - +**The Amazon Genomics CLI project has entered its End Of Life (EOL) phase**. The code is no longer actively maintained and the **Github repository will be archived on May 31 2024**. During this time, we encourage customers to migrate to [AWS HealthOmics](https://aws.amazon.com/healthomics/) to run their genomics workflows on AWS, or [reach out to their AWS account team](https://aws.amazon.com/contact-us/?nc2=h_header) for alternative solutions. While the source code of AGC will still be available after the EOL date, we will not make any updates inclusive of addressing issues or accepting Pull Requests. {{< blocks/section color="white" >}} {{% blocks/feature icon="fa fa-download" title="Download Binaries" url="https://github.com/aws/amazon-genomics-cli/releases"%}} Get compiled [releases](https://github.com/aws/amazon-genomics-cli/releases) of Amazon Genomics CLI diff --git a/site/content/en/docs/Concepts/_index.md b/site/content/en/docs/Concepts/_index.md index 59aed5d1..5ab5d178 100644 --- a/site/content/en/docs/Concepts/_index.md +++ b/site/content/en/docs/Concepts/_index.md @@ -6,6 +6,10 @@ description: > What do you need to know about Amazon Genomics CLI in order to use it - or potentially contribute to it? --- +{{% alert title="Attention" color="warning" %}} +**The Amazon Genomics CLI project has entered its End Of Life (EOL) phase**. The code is no longer actively maintained and the **Github repository will be archived on May 31 2024**. During this time, we encourage customers to migrate to [AWS HealthOmics](https://aws.amazon.com/healthomics/) to run their genomics workflows on AWS, or [reach out to their AWS account team](https://aws.amazon.com/contact-us/?nc2=h_header) for alternative solutions. While the source code of AGC will still be available after the EOL date, we will not make any updates inclusive of addressing issues or accepting Pull Requests. +{{% /alert %} + For a general introduction to the AWS Genomics CLI, refer to the [Overview]( {{< ref "/docs/Overview/" >}} ). Amazon Genomics CLI uses a handful of core concepts to abstract the deployment of infrastructure needed to run workflows and to organize diff --git a/site/content/en/docs/Contribution guidelines/_index.md b/site/content/en/docs/Contribution guidelines/_index.md index 2d066576..67064f73 100644 --- a/site/content/en/docs/Contribution guidelines/_index.md +++ b/site/content/en/docs/Contribution guidelines/_index.md @@ -6,6 +6,11 @@ description: > How to contribute to AWS Genomics CLI --- +{{% alert title="Attention" color="warning" %}} +**The Amazon Genomics CLI project has entered its End Of Life (EOL) phase**. The code is no longer actively maintained and the **Github repository will be archived on May 31 2024**. During this time, we encourage customers to migrate to [AWS HealthOmics](https://aws.amazon.com/healthomics/) to run their genomics workflows on AWS, or [reach out to their AWS account team](https://aws.amazon.com/contact-us/?nc2=h_header) for alternative solutions. While the source code of AGC will still be available after the EOL date, we will not make any updates inclusive of addressing issues or accepting Pull Requests. +{{% /alert %} + + We use Go as the main language of the AWS Genomics CLI. To interact with AWS Services we use the AWS SDK for Go v2. Infrastructure to be deployed into an AWS Account is coded as TypeScript using the AWS CDK. diff --git a/site/content/en/docs/Examples/_index.md b/site/content/en/docs/Examples/_index.md index 7039a61d..e284632c 100755 --- a/site/content/en/docs/Examples/_index.md +++ b/site/content/en/docs/Examples/_index.md @@ -8,6 +8,10 @@ description: > Amazon Genomics CLI in action! --- +{{% alert title="Attention" color="warning" %}} +**The Amazon Genomics CLI project has entered its End Of Life (EOL) phase**. The code is no longer actively maintained and the **Github repository will be archived on May 31 2024**. During this time, we encourage customers to migrate to [AWS HealthOmics](https://aws.amazon.com/healthomics/) to run their genomics workflows on AWS, or [reach out to their AWS account team](https://aws.amazon.com/contact-us/?nc2=h_header) for alternative solutions. While the source code of AGC will still be available after the EOL date, we will not make any updates inclusive of addressing issues or accepting Pull Requests. +{{% /alert %} + As part of our GitHub distribution we provide some example projects along with their workflows in the `examples/` folder. These projects are also included in the `$HOME/agc/examples` folder that is created when you install Amazon Genomics CLI. diff --git a/site/content/en/docs/Getting started/_index.md b/site/content/en/docs/Getting started/_index.md index 1b1780ef..0a467706 100644 --- a/site/content/en/docs/Getting started/_index.md +++ b/site/content/en/docs/Getting started/_index.md @@ -6,6 +6,11 @@ description: > What does your user need to know to try your project? --- +{{% alert title="Attention" color="warning" %}} +**The Amazon Genomics CLI project has entered its End Of Life (EOL) phase**. The code is no longer actively maintained and the **Github repository will be archived on May 31 2024**. During this time, we encourage customers to migrate to [AWS HealthOmics](https://aws.amazon.com/healthomics/) to run their genomics workflows on AWS, or [reach out to their AWS account team](https://aws.amazon.com/contact-us/?nc2=h_header) for alternative solutions. While the source code of AGC will still be available after the EOL date, we will not make any updates inclusive of addressing issues or accepting Pull Requests. +{{% /alert %} + + {{% pageinfo %}} The following links will help you install Amazon Genomics CLI and quickly run a demo workflow. {{% /pageinfo %}} diff --git a/site/content/en/docs/Overview/_index.md b/site/content/en/docs/Overview/_index.md index 6f66aea0..e721c831 100644 --- a/site/content/en/docs/Overview/_index.md +++ b/site/content/en/docs/Overview/_index.md @@ -6,6 +6,10 @@ description: > Amazon Genomics CLI Overview. --- +{{% alert title="Attention" color="warning" %}} +**The Amazon Genomics CLI project has entered its End Of Life (EOL) phase**. The code is no longer actively maintained and the **Github repository will be archived on May 31 2024**. During this time, we encourage customers to migrate to [AWS HealthOmics](https://aws.amazon.com/healthomics/) to run their genomics workflows on AWS, or [reach out to their AWS account team](https://aws.amazon.com/contact-us/?nc2=h_header) for alternative solutions. While the source code of AGC will still be available after the EOL date, we will not make any updates inclusive of addressing issues or accepting Pull Requests. +{{% /alert %} + ## What is the Amazon Genomics CLI? Amazon Genomics CLI is an open source tool for genomics and life science customers that simplifies and automates the diff --git a/site/content/en/docs/Reference/_index.md b/site/content/en/docs/Reference/_index.md index 279320f1..17384837 100644 --- a/site/content/en/docs/Reference/_index.md +++ b/site/content/en/docs/Reference/_index.md @@ -6,4 +6,8 @@ description: > Command reference. --- +{{% alert title="Attention" color="warning" %}} +**The Amazon Genomics CLI project has entered its End Of Life (EOL) phase**. The code is no longer actively maintained and the **Github repository will be archived on May 31 2024**. During this time, we encourage customers to migrate to [AWS HealthOmics](https://aws.amazon.com/healthomics/) to run their genomics workflows on AWS, or [reach out to their AWS account team](https://aws.amazon.com/contact-us/?nc2=h_header) for alternative solutions. While the source code of AGC will still be available after the EOL date, we will not make any updates inclusive of addressing issues or accepting Pull Requests. +{{% /alert %} + ## Command Reference diff --git a/site/content/en/docs/Tutorials/_index.md b/site/content/en/docs/Tutorials/_index.md index 28eb6b4f..193984c9 100755 --- a/site/content/en/docs/Tutorials/_index.md +++ b/site/content/en/docs/Tutorials/_index.md @@ -8,6 +8,9 @@ description: > Work through some end to end examples. --- +{{% alert title="Attention" color="warning" %}} +**The Amazon Genomics CLI project has entered its End Of Life (EOL) phase**. The code is no longer actively maintained and the **Github repository will be archived on May 31 2024**. During this time, we encourage customers to migrate to [AWS HealthOmics](https://aws.amazon.com/healthomics/) to run their genomics workflows on AWS, or [reach out to their AWS account team](https://aws.amazon.com/contact-us/?nc2=h_header) for alternative solutions. While the source code of AGC will still be available after the EOL date, we will not make any updates inclusive of addressing issues or accepting Pull Requests. +{{% /alert %} The following are **complete worked examples** made up of **multiple tasks** that guide you through a relatively simple but realistic scenarios using Amazon Genomics CLI. diff --git a/site/content/en/docs/Workflow engines/Filesystems/_index.md b/site/content/en/docs/Workflow engines/Filesystems/_index.md index 0989247e..262e17c6 100644 --- a/site/content/en/docs/Workflow engines/Filesystems/_index.md +++ b/site/content/en/docs/Workflow engines/Filesystems/_index.md @@ -8,6 +8,10 @@ description: > Workflow Filesystems --- +{{% alert title="Attention" color="warning" %}} +**The Amazon Genomics CLI project has entered its End Of Life (EOL) phase**. The code is no longer actively maintained and the **Github repository will be archived on May 31 2024**. During this time, we encourage customers to migrate to [AWS HealthOmics](https://aws.amazon.com/healthomics/) to run their genomics workflows on AWS, or [reach out to their AWS account team](https://aws.amazon.com/contact-us/?nc2=h_header) for alternative solutions. While the source code of AGC will still be available after the EOL date, we will not make any updates inclusive of addressing issues or accepting Pull Requests. +{{% /alert %} + The tasks in a workflow require a common filesystem or scratch space where the outputs of tasks can be written so they are available to the inputs of dependent tasks in the same workflow. The following pages provide details on the engine filesystems that can be deployed by Amazon Genomics CLI. diff --git a/site/content/en/docs/Workflow engines/_index.md b/site/content/en/docs/Workflow engines/_index.md index 50999faf..c4db3142 100644 --- a/site/content/en/docs/Workflow engines/_index.md +++ b/site/content/en/docs/Workflow engines/_index.md @@ -8,6 +8,10 @@ description: > Supported Workflow Engines --- +{{% alert title="Attention" color="warning" %}} +**The Amazon Genomics CLI project has entered its End Of Life (EOL) phase**. The code is no longer actively maintained and the **Github repository will be archived on May 31 2024**. During this time, we encourage customers to migrate to [AWS HealthOmics](https://aws.amazon.com/healthomics/) to run their genomics workflows on AWS, or [reach out to their AWS account team](https://aws.amazon.com/contact-us/?nc2=h_header) for alternative solutions. While the source code of AGC will still be available after the EOL date, we will not make any updates inclusive of addressing issues or accepting Pull Requests. +{{% /alert %} + The following pages provide details on the workflow engines that are currently supported by Amazon Genomics CLI.