BioAnalyze Terraform AWS PCluster AMIs Module

Terraform Github Project Template

This is a GitHub project template. To get started using this structure click the ' Use this Template' button on the main github repo page.

Update the README.yaml to reflect this project.

This project wouldn't be possible without open source software. The conventions used in the terraform recipes come from the CloudPosse group.

---

This project is part of the "BioAnalyze" project, which aims to make High Performance Compute Architecture accessible to everyone.

It's 100% Open Source and licensed under the APACHE2 .

Data Science Infrastructure on AWS

** IMPORTANT:** We do not pin modules to versions in our examples because of the difficulty of keeping the versions in the documentation in sync with the latest released versions. We highly recommend that in your code you pin the version to the exact version you are using so that your infrastructure remains stable, and update versions in a systematic way so that they do not catch you by surprise.

Also, because of a bug in the Terraform registry (hashicorp/terraform#21417) , the registry shows many of our inputs as required when in fact they are optional. The table below correctly indicates which inputs are required.

For a complete example, see examples/complete .

For automated tests of the complete example using bats and Terratest ( which tests and deploys the example on AWS) , see test .

module "eks" {
  source = "dabble-of-devops-bioanalyze/eks-jupyterhub/aws"

  region     = var.region
  vpc_id     = var.vpc_id
  subnet_ids = var.subnet_ids

  oidc_provider_enabled             = true
  cluster_encryption_config_enabled = true

  context = module.this.context
}

Examples

Here is an example of using this module:

• examples/complete

  complete example of using this module

Makefile Targets

Available targets:

  help                                Help screen
  help/all                            Display help for all targets
  help/short                          This help short screen
  lint                                Lint terraform code

Requirements

Name	Version
terraform	> = 0.13
local	> = 1.2
random	> = 2.2

Providers

Name	Version
random	> = 2.2

Modules

Name	Source	Version
this	cloudposse/label/null	0.25.0

Resources

Name	Type
random_integer.example	resource

Inputs

Name	Description	Type	Default	Required
additional_tag_map	Additional key-value pairs to add to each map in tags_as_list_of_maps. Not added to tags or id. This is for some rare cases where resources want additional configuration of tags and therefore take a list of maps with tag key, value, and additional configuration.	map(string)	{}	no
attributes	ID element. Additional attributes (e.g. workers or cluster) to add to id, in the order they appear in the list. New attributes are appended to the end of the list. The elements of the list are joined by the delimiter and treated as a single ID element.	list(string)	[]	no
aws_route53_record_name	Record name to add to aws_route_53. Must be a valid subdomain - www,app,etc	string	"www"	no
aws_route53_zone_name	Name of the zone to add records. Do not forget the trailing '.' - 'test.com.'	string	"test.com."	no
context	Single object for setting entire context at once. See description of individual variables for details. Leave string and numeric variables as null to use default value. Individual variable settings (non-null) override settings in context object, except for attributes, tags, and additional_tag_map, which are merged.	any	{ "additional_tag_map": {}, "attributes": [], "delimiter": null, "descriptor_formats": {}, "enabled": true, "environment": null, "id_length_limit": null, "label_key_case": null, "label_order": [], "label_value_case": null, "labels_as_tags": [ "unset" ], "name": null, "namespace": null, "regex_replace_chars": null, "stage": null, "tags": {}, "tenant": null }	no
delimiter	Delimiter to be used between ID elements. Defaults to - (hyphen). Set to "" to use no delimiter at all.	string	null	no
descriptor_formats	Describe additional descriptors to be output in the descriptors output map. Map of maps. Keys are names of descriptors. Values are maps of the form {<br> format = string<br> labels = list(string)<br>} (Type is any so the map values can later be enhanced to provide additional options.) format is a Terraform format string to be passed to the format() function. labels is a list of labels, in order, to pass to format() function. Label values will be normalized before being passed to format() so they will be identical to how they appear in id. Default is {} (descriptors output will be empty).	any	{}	no
eks_cluster_id	EKS Cluster Id - This cluster must exist.	string	n/a	yes
eks_cluster_oidc_issuer_url	URL to the oidc issuer. The cluster must have been created with : oidc_provider_enabled = true	string	n/a	yes
enable_ssl	Enable SSL Support?	bool	true	no
enabled	Set to false to prevent the module from creating any resources	bool	null	no
environment	ID element. Usually used for region e.g. 'uw2', 'us-west-2', OR role 'prod', 'staging', 'dev', 'UAT'	string	null	no
helm_release_chart	helm release chart	string	n/a	yes
helm_release_create_namespace	n/a	bool	true	no
helm_release_name	helm release name	string	n/a	yes
helm_release_namespace	helm release namespace	string	"default"	no
helm_release_repository	helm release chart repository	string	n/a	yes
helm_release_values_dir	Directory to put rendered values template files or additional keys. Should be helm_charts/{helm_release_name}	string	"helm_charts"	no
helm_release_values_files	helm release values files - paths values files to add to helm install --values {}	list(string)	[]	no
helm_release_version	helm release version	string	n/a	yes
helm_release_wait	n/a	bool	true	no
id_length_limit	Limit id to this many characters (minimum 6). Set to 0 for unlimited length. Set to null for keep the existing setting, which defaults to 0. Does not affect id_full.	number	null	no
label_key_case	Controls the letter case of the tags keys (label names) for tags generated by this module. Does not affect keys of tags passed in via the tags input. Possible values: lower, title, upper. Default value: title.	string	null	no
label_order	The order in which the labels (ID elements) appear in the id. Defaults to ["namespace", "environment", "stage", "name", "attributes"]. You can omit any of the 6 labels ("tenant" is the 6th), but at least one must be present.	list(string)	null	no
label_value_case	Controls the letter case of ID elements (labels) as included in id, set as tag values, and output by this module individually. Does not affect values of tags passed in via the tags input. Possible values: lower, title, upper and none (no transformation). Set this to title and set delimiter to "" to yield Pascal Case IDs. Default value: lower.	string	null	no
labels_as_tags	Set of labels (ID elements) to include as tags in the tags output. Default is to include all labels. Tags with empty values will not be included in the tags output. Set to [] to suppress all generated tags. **
Notes:** The value of the name tag, if included, will be the id, not the name. Unlike other null-label inputs, the initial setting of labels_as_tags cannot be changed in later chained modules. Attempts to change it will be silently ignored.	set(string)	[ "default" ]	no
letsencrypt_email	Email to use for https setup. Not needed unless enable_ssl	string	"hello@gmail.com"	no
name	ID element. Usually the component or solution name, e.g. 'app' or 'jenkins'. This is the only ID element not also included as a tag. The "name" tag is set to the full id string. There is no tag with the value of the name input.	string	null	no
namespace	ID element. Usually an abbreviation of your organization name, e.g. 'eg' or 'cp', to help ensure generated IDs are globally unique	string	null	no
regex_replace_chars	Terraform regular expression (regex) string. Characters matching the regex will be removed from the ID elements. If not set, "/[^a-zA-Z0-9-]/" is used to remove all characters other than hyphens, letters and digits.	string	null	no
region	AWS Region	string	"us-east-1"	no
stage	ID element. Usually used to indicate role, e.g. 'prod', 'staging', 'source', 'build', 'test', 'deploy', 'release'	string	null	no
tags	Additional tags (e.g. {'BusinessUnit': 'XYZ'}). Neither the tag keys nor the tag values will be modified by this module.	map(string)	{}	no
tenant	ID element _(Rarely used, not included by default)_. A customer identifier, indicating who this instance of a resource is for	string	null	no

Outputs

Name	Description
example	Example output
id	ID of the created example
random	Stable random number for this example

Share the Love

Like this project? Please give it a ★ on our GitHub! ( it helps ** a lot**)

Related Projects

Check out these related projects.

• terraform-aws-eks-autoscaling

  Terraform module to provision an Autoscaling EKS Cluster. Acts as a wrapper around cloudposse/terraform-aws-eks-cluster and cloudposse/terraform-aws-eks-node-groups

• terraform-aws-eks-cluster

  Terraform module to deploy an AWS EKS Cluster.

• terraform-aws-eks-node-group

  Terraform module to provision an EKS Node Group

• Zero to Kubernetes

  JupyterHub allows users to interact with a computing environment through a webpage. As most devices have access to a web browser, JupyterHub makes it is easy to provide and standardize the computing environment for a group of people ( e.g., for a class of students or an analytics team) .

This project will help you set up your own JupyterHub on a cloud/on-prem k8s environment and leverage its scalable nature to support a large group of users. Thanks to Kubernetes, we are not tied to a specific cloud provider.

• Dask Gateway

  Dask Gateway provides a secure, multi-tenant server for managing Dask clusters. It allows users to launch and use Dask clusters in a shared, centrally managed cluster environment, without requiring users to have direct access to the underlying cluster backend ( e.g. Kubernetes, Hadoop/YARN, HPC Job queues, etc…) .

• DaskHub

  This chart provides a multi-user, Dask-Gateway enabled JupyterHub. It combines the JupyterHub and Dask Gateway helm charts.

• Dask

  Dask is a flexible library for parallel computing in Python.

• terraform-aws-ec2-autoscale-group

  Terraform module to provision Auto Scaling Group and Launch Template on AWS

• terraform-aws-ec2-instance

  Terraform module for providing a general purpose EC2 instance

• terraform-aws-ec2-instance-group

  Terraform module for provisioning multiple general purpose EC2 hosts for stateful applications

• terraform-null-label

  Terraform module designed to generate consistent names and tags for resources. Use terraform-null-label to implement a strict naming convention.

References

For additional context, refer to some of these links.

• Terraform Standard Module Structure

  HashiCorp's standard module structure is a file and directory layout we recommend for reusable modules distributed in separate repositories.

• Terraform Module Requirements

  HashiCorp's guidance on all the requirements for publishing a module. Meeting the requirements for publishing a module is extremely easy.

• Terraform random_integer Resource

  The resource random_integer generates random values from a given range, described by the min and max attributes of a given resource.

• Terraform Version Pinning

  The required_version setting can be used to constrain which versions of the Terraform CLI can be used with your configuration

Help

** Got a question?** We got answers.

File a GitHub issue , send us an jillian@dabbleofdevops.com.

Bioinformatics Infrastructure on AWS for Startups

I'll help you build your data science cloud infrastructure from the ground up so you can own it using open source software. Then I'll show you how to operate it and stick around for as long as you need us.

Learn More

Work directly with me via email, slack, and video conferencing.

• ** Scientific Workflow Automation and Optimization.** Got workflows that are giving you trouble? Let's work together to ensure that your analyses run with or without your scientists being fully caffeinated.
• ** High Performance Compute Infrastructure.** Highly available, auto scaling clusters to analyze * all the ( bioinformatics related!) things* . All setups are completely integrated with your workflow system of choice, whether that is Airflow, Prefect, Snakemake or Nextflow.
• ** Kubernetes and AWS Batch Setup for Apache Airflow** Orchestrate your Bioinformatics Workflows with Apache Airflow. Get full auditing, SLA, logging and monitoring for your workflows running on AWS Batch.
• ** High Performance Compute Setup that Int** You'll have built-in governance with accountability and audit logs for all changes.
• ** Docker Images** Get advice and hands on training for your team to build complex software stacks onto docker images.
• ** Training.** You'll receive hands-on training so your team can operate what we build.
• ** Questions.** You'll have a direct line of communication between our teams via a Shared Slack channel.
• ** Troubleshooting.** You'll get help to triage when things aren' t working.
• ** Bug Fixes.** We'll rapidly work with you to fix any bugs in our projects.

Contributing

Bug Reports & Feature Requests

Please use the issue tracker to report any bugs or file feature requests.

Developing

If you are interested in being a contributor and want to get involved in developing this project or help out with other projects, I would love to hear from you! Shoot me an email at jillian@dabbleofdevops.com.

In general, PRs are welcome. We follow the typical " fork-and-pull" Git workflow.

1. ** Fork** the repo on GitHub
2. ** Clone** the project to your own machine
3. ** Commit** changes to your own branch
4. ** Push** your work back up to your fork

Submit a ** Pull Request** so that we can review your changes

Developer Notes

The README.md is created using the standard CloudPosse template that has been modified to use BioAnalyze information and URLs, and other documentation is generated using jupyter-book .

Terraform code does not render properly when using the literalinclude directive, so instead we use pygmentize to render it to html which is included directly.

.. raw:: html
   :file: ./_html/main.tf.html

** NOTE:** Be sure to merge the latest changes from " upstream" before making a pull request!

Copyrights

Copyright © 2020-2021 Dabble of DevOps, SCorp

License

See LICENSE for full details.

Licensed to the Apache Software Foundation (ASF) under one
or more contributor license agreements.  See the NOTICE file
distributed with this work for additional information
regarding copyright ownership.  The ASF licenses this file
to you under the Apache License, Version 2.0 (the
"License"); you may not use this file except in compliance
with the License.  You may obtain a copy of the License at

  https://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing,
software distributed under the License is distributed on an
"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
KIND, either express or implied.  See the License for the
specific language governing permissions and limitations
under the License.

Trademarks

All other trademarks referenced herein are the property of their respective owners.

Contributors

|
Jillian Rowe |

Learn more at Dabble of DevOps

Sponsor

BioAnalyze is and will always be open source. If you've found any of these resources helpful, please consider donating to the continued development of BioAnalyze.

Sponsor BioAnalyze