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README.md.gotmpl
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{{- defineDatasource "config" .Env.README_YAML | regexp.Replace ".*" "" -}}
{{- defineDatasource "includes" .Env.README_INCLUDES | regexp.Replace ".*" "" -}}
{{- $deprecated := has (ds "config") "deprecated" }}
<!-- markdownlint-disable -->
{{- if $deprecated }}
# (deprecated) {{(ds "config").name}}{{ if gt (len (ds "config").name) 23 }}{{ print "\n\n" }}{{ end }}
{{- else }}
# {{(ds "config").name }}{{ if gt (len (ds "config").name) 34 }}{{ print "\n\n" }}{{ end }}
{{- end }}
{{- if $deprecated }}[](#deprecated){{ end }}
{{- if has (ds "config") "badges" }}
{{- range $badge := (ds "config").badges }}
{{- printf " [](%s)" $badge.name $badge.image $badge.url }}
{{- end }}
{{- end }}
<!-- markdownlint-restore -->
<!--
** DO NOT EDIT THIS FILE
**
** This file was automatically generated by the `build-harness`.
** 1) Make all changes to `README.yaml`
** 2) Run `make init` (you only need to do this once)
** 3) Run`make readme` to rebuild this file.
**
** (We maintain HUNDREDS of open source projects. This is how we maintain our sanity.)
**
-->
{{ if has (ds "config") "logo" }}
.logo }})
{{- end -}}
{{- if $deprecated }}
## Deprecated
{{ if has (ds "config").deprecated "notice" }}
{{- (ds "config").deprecated.notice }}
{{- else }}
This module is no longer actively maintained
{{- end }}
{{- if (file.Exists "main.tf") }}
{{- end }}
{{ if has (ds "config") "description" }}
### Historical Description
{{(ds "config").description }}
{{- end }}
{{- else }}
{{- if has (ds "config") "description" }}
{{ (ds "config").description }}
{{- end }}
{{- end }}
---
This project {{ if $deprecated }}was{{ else }}is{{ end }} part of the ["BioAnalyze"](https://www.dabbleofdevops.com/biohub) project, which aims to make High Performance Compute Architecture accessible to everyone.
{{ if eq (ds "config").license "APACHE2" }}
It's 100% Open Source and licensed under the [APACHE2](LICENSE).
{{ end }}
{{ if eq (ds "config").license "CC-BY-NC-SA-4.0" }}
It's 100% Open Source and licensed under the [Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License](LICENSE).
<a href="https://creativecommons.org/licenses/by-nc-sa/4.0/"><img title="Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License" src="static/images/cc-by-nc-sa.png" width="150" /></a>
{{ end }}
{{ if eq (ds "config").license "MIT" }}
It's 100% Open Source and licensed under the [MIT](LICENSE).
{{ end }}
{{ if eq (ds "config").license "ISC" }}
It's 100% Open Source and licensed under the [Internet Systems Consortium](LICENSE).
{{ end }}
{{ if eq (ds "config").license "GPL3" }}
It's 100% Open Source and licensed under the [GNU General Public License](LICENSE).
{{ end }}
## Data Science Infrastructure on AWS
{{ if has (ds "config") "screenshots" }}
## Screenshots
{{ range $screenshot := (ds "config").screenshots }}
{{ printf "\n*%s*" $screenshot.name $screenshot.url $screenshot.description }}{{ end }}
{{- end }}
{{ if has (ds "config") "introduction" }}
## Introduction
{{ (ds "config").introduction }}
{{ end }}
{{ if (file.Exists "main.tf") }}
**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](https://github.com/hashicorp/terraform/issues/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.
{{end}}
{{ (ds "config").usage -}}
{{ if not $deprecated -}}
{{ if has (ds "config") "quickstart" -}}
## Quick Start
{{ (ds "config").quickstart -}}
{{ end }}
{{ if has (ds "config") "examples" }}
## Examples
{{(ds "config").examples }}
{{ end }}
{{ if has (ds "config") "include" }}
{{ range $file := (datasource "config").include -}}
{{ (include "includes" $file) }}
{{- end }}
{{- end }}
{{ if has (ds "config") "related" }}
## Share the Love
Like this project? Please give it a ★ on [our GitHub]({{ printf "https://github.com/%s" (ds "config").github_repo}})! (it helps **a lot**)
{{ end }}
{{ if has (ds "config") "related" }}
## Related Projects
Check out these related projects.
{{ range $related := (ds "config").related }}
{{ printf "- [%s](%s) - %s" $related.name $related.url $related.description }}{{ end }}
{{- end}}
{{- end}}
{{ if has (ds "config") "references" }}
## References
For additional context, refer to some of these links.
{{ range $reference := (ds "config").references }}
{{ printf "- [%s](%s) - %s" $reference.name $reference.url $reference.description }}{{ end }}
{{ end}}
## Help
**Got a question?** We got answers.
File a GitHub [issue]({{ printf "https://github.com/%s/issues" (ds "config").github_repo}}), 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](https://www.dabbleofdevops.com)
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.
{{ if not $deprecated -}}
## Contributing
### Bug Reports & Feature Requests
Please use the [issue tracker]({{ printf "https://github.com/%s/issues" (ds "config").github_repo}}) 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
5. Submit a **Pull Request** so that we can review your changes
#### Developer Notes
The `README.md` is created using the standard [CloudPosse](https://github.com/cloudposse/terraform-example-module) template that has been modified to use BioAnalyze information and URLs, and other documentation is generated using [jupyter-book](https://jupyterbook.org/).
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!
{{ end }}
{{ if has (ds "config") "copyrights" }}
## Copyrights
{{ range $copyright := (ds "config").copyrights -}}
{{ printf "Copyright © %s-%d [%s](%s)\n" $copyright.year time.Now.Year $copyright.name $copyright.url }}
{{ end }}
{{ else }}
## Copyright
Copyright © 2017-{{ time.Now.Year }} [Dabble of DevOps Consulting](https://cpco.io/copyright)
{{ end}}
{{ if eq (ds "config").license "APACHE2" }}
## License
[](https://opensource.org/licenses/Apache-2.0)
See [LICENSE](LICENSE) for full details.
```text
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.
```
{{ end }}
{{ if eq (ds "config").license "CC-BY-NC-SA-4.0" }}
## License
[](https://creativecommons.org/licenses/by-nc-sa/4.0/)
<a href="https://creativecommons.org/licenses/by-nc-sa/4.0/"><img title="Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License" src="https://docs.cloudposse.com/images/cc-by-nc-sa.png" width="150" /></a>
This material may only be distributed subject to the terms and conditions set forth in the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License or later with the restrictions noted below (the latest version of the license is presently available at <https://creativecommons.org/licenses/by-nc-sa/4.0/>).
**Attribution** You must attribute the work in the manner specified by the author or licensor.
**Noncommercial** The licensor permits others to copy, distribute and transmit the work. In return, licensees may not use the work for commercial purposes — unless they get the licensor's permission.
**Share Alike** The licensor permits others to distribute derivative works only under the same license or one compatible with the one that governs the licensor's work.
## Distribution
Distribution of substantively modified versions of this document is prohibited without the explicit permission of the copyright holder.
Distribution of the work or derivative of the work in any standard (paper) book form for commercial purposes is prohibited unless prior permission is obtained from the copyright holder.
{{ end }}
{{ if eq (ds "config").license "MIT" }}
## License
[](https://opensource.org/licenses/MIT)
```text
The MIT License (MIT)
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
Source: <https://opensource.org/licenses/MIT>
```
{{ end }}
{{ if eq (ds "config").license "ISC" }}
## License
[](https://opensource.org/licenses/ISC)
```text
ISC License (ISC)
Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies.
THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
Source: <https://opensource.org/licenses/ISC>
```
{{ end }}
{{ if eq (ds "config").license "GPL3" }}
## License
[](https://www.gnu.org/licenses/gpl-3.0)
```text
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
```
{{ end }}
## Trademarks
All other trademarks referenced herein are the property of their respective owners.
{{ if has (datasource "config") "contributors" }}
### Contributors
<!-- markdownlint-disable -->
| {{ range $contributor := (ds "config").contributors }}{{ printf " [![%s][%s_avatar]][%s_homepage]<br/>[%s][%s_homepage] |" $contributor.name $contributor.github $contributor.github $contributor.name $contributor.github}}{{ end }}
<!-- markdownlint-restore -->
{{ range $contributor := (ds "config").contributors -}}
{{- if has $contributor "homepage" }}
{{ printf " [%s_homepage]: %s" $contributor.github $contributor.homepage }}
{{ else -}}
{{ printf " [%s_homepage]: https://github.com/%s" $contributor.github $contributor.github }}
{{ end -}}
{{ if has $contributor "avatar" }}{{ printf " [%s_avatar]: %s" $contributor.github $contributor.avatar }}
{{ else -}}
{{ printf " [%s_avatar]: https://img.cloudposse.com/150x150/https://github.com/%s.png" $contributor.github $contributor.github }}
{{- end }}
{{ end }}
{{ end }}
{{- $utm_link := printf "%%s?utm_source=%s&utm_medium=%s&utm_campaign=%s&utm_content=%s" "github" "readme" (ds "config").github_repo "%s" -}}
Learn more at [Dabble of DevOps](https://www.dabbleofdevops.com)
## 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](https://github.com/sponsors/dabble-of-devops-bioanalyze)
[logo]: https://cloudposse.com/logo-300x69.svg
[docs]: {{ printf $utm_link "https://cpco.io/docs" "docs" }}
[website]: {{ printf $utm_link "https://cpco.io/homepage" "website" }}
[github]: {{ printf $utm_link "https://cpco.io/github" "github" }}
[jobs]: {{ printf $utm_link "https://cpco.io/jobs" "jobs" }}
[hire]: {{ printf $utm_link "https://cpco.io/hire" "hire" }}
[slack]: {{ printf $utm_link "https://cpco.io/slack" "slack" }}
[linkedin]: {{ printf $utm_link "https://cpco.io/linkedin" "linkedin" }}
[twitter]: {{ printf $utm_link "https://cpco.io/twitter" "twitter" }}
[testimonial]: {{ printf $utm_link "https://cpco.io/leave-testimonial" "testimonial" }}
[office_hours]: {{ printf $utm_link "https://cloudposse.com/office-hours" "office_hours" }}
[newsletter]: {{ printf $utm_link "https://cpco.io/newsletter" "newsletter" }}
[discourse]: {{ printf $utm_link "https://ask.sweetops.com/" "discourse" }}
[email]: {{ printf $utm_link "https://cpco.io/email" "email" }}
[commercial_support]: {{ printf $utm_link "https://cpco.io/commercial-support" "commercial_support" }}
[we_love_open_source]: {{ printf $utm_link "https://cpco.io/we-love-open-source" "we_love_open_source" }}
[terraform_modules]: {{ printf $utm_link "https://cpco.io/terraform-modules" "terraform_modules" }}
[readme_header_img]: {{ printf "https://cloudposse.com/readme/header/img" }}
[readme_header_link]: {{ printf $utm_link "https://cloudposse.com/readme/header/link" "readme_header_link" }}
[readme_footer_img]: {{ printf "https://cloudposse.com/readme/footer/img" }}
[readme_footer_link]: {{ printf $utm_link "https://cloudposse.com/readme/footer/link" "readme_footer_link" }}
[readme_commercial_support_img]: {{ printf "https://cloudposse.com/readme/commercial-support/img" }}
[readme_commercial_support_link]: {{ printf $utm_link "https://cloudposse.com/readme/commercial-support/link" "readme_commercial_support_link" }}
[share_twitter]: {{ printf "https://twitter.com/intent/tweet/?text=%s&url=https://github.com/%s" ((ds "config").name | regexp.Replace " " "+") (ds "config").github_repo }}
[share_linkedin]: {{ printf "https://www.linkedin.com/shareArticle?mini=true&title=%s&url=https://github.com/%s" ((ds "config").name | regexp.Replace " " "+") (ds "config").github_repo }}
[share_reddit]: {{ printf "https://reddit.com/submit/?url=https://github.com/%s" (ds "config").github_repo }}
[share_facebook]: {{ printf "https://facebook.com/sharer/sharer.php?u=https://github.com/%s" (ds "config").github_repo }}
[share_googleplus]: {{ printf "https://plus.google.com/share?url=https://github.com/%s" (ds "config").github_repo }}
[share_email]: {{ printf "mailto:?subject=%s&body=https://github.com/%s" ((ds "config").name | regexp.Replace " " "+") (ds "config").github_repo }}
[beacon]: {{ printf "https://ga-beacon.cloudposse.com/UA-76589703-4/%s?pixel&cs=github&cm=readme&an=%s" (ds "config").github_repo (filepath.Base ((ds "config").github_repo)) }}