Initial Documentation Fix by GPelayo · Pull Request #34 · ucsc-cgp/cgp-deployment

GPelayo · 2018-07-06T23:27:50Z

No description provided.

mikebaumann

Thanks for your work on this, @GPelayo!
Please address the comments I added and let me know when it is ready for re-review.

mikebaumann · 2018-07-09T23:22:08Z

README.md

@@ -1,93 +1,177 @@
-# cgp-deployment
+# cgp-deployment (Commons Edition)


Change:
Commons Edition
to:
Data Commons/STAGE Edition

mikebaumann · 2018-07-09T23:26:17Z

README.md

 ## About

-This repository contains our Docker-compose and setup bootstrap scripts used to create a deployment of the [UCSC Genomic Institute's](http://ucsc-cgl.org) Computational Genomics Platform for AWS. It uses, supports, and drives development of several key GA4GH APIs and open source projects. In many ways it is the generalization of the [PCAWG](https://dcc.icgc.org/pcawg) cloud infrastructure developed for that project and a potential reference implementation for the [NIH Commons](https://datascience.nih.gov/commons) concept.
+This repository contains our Docker-compose and setup bootstrap scripts used to create a deployment of the [UCSC Genomic Institute's](http://ucsc-cgl.org)


Change:
http://ucsc-cgl.org
to:
https://commons.ucsc-cgp.org/

mikebaumann · 2018-07-09T23:28:27Z

README.md


-This repository contains our Docker-compose and setup bootstrap scripts used to create a deployment of the [UCSC Genomic Institute's](http://ucsc-cgl.org) Computational Genomics Platform for AWS. It uses, supports, and drives development of several key GA4GH APIs and open source projects. In many ways it is the generalization of the [PCAWG](https://dcc.icgc.org/pcawg) cloud infrastructure developed for that project and a potential reference implementation for the [NIH Commons](https://datascience.nih.gov/commons) concept.
+This repository contains our Docker-compose and setup bootstrap scripts used to create a deployment of the [UCSC Genomic Institute's](http://ucsc-cgl.org)
+Computational Genomics Platform for AWS. It uses, supports, and drives development of several key GA4GH APIs and open source projects.


Change:
for AWS.
to:
for AWS and GCP.

mikebaumann · 2018-07-09T23:32:29Z

README.md

-This repository contains our Docker-compose and setup bootstrap scripts used to create a deployment of the [UCSC Genomic Institute's](http://ucsc-cgl.org) Computational Genomics Platform for AWS. It uses, supports, and drives development of several key GA4GH APIs and open source projects. In many ways it is the generalization of the [PCAWG](https://dcc.icgc.org/pcawg) cloud infrastructure developed for that project and a potential reference implementation for the [NIH Commons](https://datascience.nih.gov/commons) concept.
+This repository contains our Docker-compose and setup bootstrap scripts used to create a deployment of the [UCSC Genomic Institute's](http://ucsc-cgl.org)
+Computational Genomics Platform for AWS. It uses, supports, and drives development of several key GA4GH APIs and open source projects.
+In many ways it is the generalization of the [PCAWG](https://dcc.icgc.org/pcawg) cloud infrastructure developed for that project and a potential reference implementation for the [NIH Commons](https://datascience.nih.gov/commons) concept.


Add:
It is currently being used in the NIH Data Commons Pilot and NHLBI Data STAGE programs.

mikebaumann · 2018-07-09T23:35:52Z

README.md

 These components are setup with the install process available in this repository:

-* [Boardwalk](boardwalk/README.md): our file browsing portal on top of Redwood
+* [Boardwalk](boardwalk/README.md): our file browsing portal on top of the Blue Box


Change:
the Blue Box
to:
the HCA/DataBiosphere Data Storage System (DSS).
This includes installation of the the Azul web service and the cgp-dashboard service.

mikebaumann · 2018-07-09T23:44:51Z

README.md

+line tool to create a host. We will refer to this as the host VM throughout the rest of the documentation. 
+It will run the Docker containers for all of the components listed below.
+
+9. Select the region in AWS Console top toolbar. **Note** We have had problems when uploading big files to Virginia (~25GB).


All these steps are numbered "9."
Please correct the numbering.

Markdown autocorrects the numbering, so they are numbered in order. This allows me to add or remove steps without updating numbering.

mikebaumann · 2018-07-09T23:46:47Z

README.md

+line tool to create a host. We will refer to this as the host VM throughout the rest of the documentation. 
+It will run the Docker containers for all of the components listed below.
+
+9. Select the region in AWS Console top toolbar. **Note** We have had problems when uploading big files to Virginia (~25GB).


Change "Virginia" to "AWS region us-east-1 (N. Virginia)"

mikebaumann · 2018-07-09T23:48:37Z

README.md

+9. Select the region in AWS Console top toolbar. **Note** We have had problems when uploading big files to Virginia (~25GB).
+    If possible, set up your AWS anywhere else but Virginia. Preferrably US-West-2 (Oregon).
+9. In the AWS Web Console Top toolbar, Click on the **Services** > **EC2** (Under the **Compute** submenu)
+    - **Note**:  Know which region to using in AWS. **Note** We have had problems when uploading big files to Virginia (~25GB).


The note re. Virginia is a redundant duplicate of the same note just above.

mikebaumann · 2018-07-10T00:01:36Z

README.md

+|ALL TCP|TCP|0 - 65535|\<Name of your Security Group>|
+
+### 4. Create your Host VM's Subdomain
+Now we need to create a subdomain and link it to for Host VM. Your subdomain should contain your.


This sentence is incomplete:
Your subdomain should contain your.

mikebaumann · 2018-07-10T00:04:00Z

README.md

+### 1 .Before Installation
+
+9. Before you start deploying make sure the following components are already setup
+    - Dos Azul Lambda


Add to list:
HCA/DataBiosphere Data Storage System(DSS)
DataBiosphere Azul indexer (for Commons)

jessebrennan

These are great doc instructions! Really clear and easy to follow. 👍

I pushed some minor adjustments and have a couple questions in the review, but otherwise this looks great!

jessebrennan · 2018-07-16T20:07:30Z

README.md

+
+### 4. Create your Host VM's Subdomain
+Now we need to create a subdomain and link it to for Host VM. Your subdomain should contain your name.
+So if your name is Bob, your subdomain should be `bob.ucsc-cgp-dev.org`.


Is this really the protocol? What if there's multiple Bobs (or Michaels)?

That's a good question. There isn't a strict protocol for subdomain naming and looking at the old documentation, it doesn't say that you can only use your name as the subdomain. Everyone just uses their name.
So maybe those directions should be something like...

Your subdomain should be your name, project, or any name that will help you identify the url. So if you want to use your name and your name is Bob, your subdomain should be `bob.ucsc-cgp-dev.org`

jessebrennan · 2018-07-16T20:09:15Z

README.md

+9. Click on **Hosted Zones** in the sidebar.
+9. In the table, click on **ucsc-cgp-dev.org.** under the **Domain Name** column.
+9. Click on the Blue **Create Record Set** button.
+9. A form should appear on the right side of the screen. Put in your name in the **Name** text box in the form.


Again, full name? first name?

mikebaumann

Thanks, Geryl -- this looks really good!
Just a couple small comments, then I think it is good to go!

mikebaumann · 2018-07-17T18:44:28Z

README.md

+### 1. Before Installation
+
+1. Before you start deploying make sure the following components are already setup
+    - DOS Azul Lambda


Please reorder as follows (the (partial) ordering in which they would need to be installed):

HCA/DataBiosphere Data Storage System(DSS)

DataBiosphere Azul indexer (for Commons)

DOS Azul Lambda

Boardwalk README for instructions on how to setup the external components.

Bagit Firecloud Lambda

mikebaumann · 2018-07-17T18:50:50Z

README.md

+    1. The Google Client Secret when you created the Google App for Boardwalk
+    1. The Google Site Verification Code from the Boardwalk setup
+    1. The url of the Bagit Firecloud Lambda
+    1. The url of the Dos Azul Lambda


Change:

The url of the Dos Azul Lambda

to:

The URL of the DOS Azul Lambda (aka DOS DSS service)

mikebaumann

Thanks, Geryl!

Initial Dox Fix Commit

e5a4e1c

GPelayo requested a review from mikebaumann July 6, 2018 23:27

ghost assigned GPelayo Jul 6, 2018

ghost added the in progress label Jul 6, 2018

mikebaumann suggested changes Jul 10, 2018

View reviewed changes

Corrected Updated Docs

78ac291

GPelayo requested a review from jessebrennan July 16, 2018 18:50

jessebrennan added 3 commits July 16, 2018 12:47

Start numbered list from 1 instead of 9

72239f8

Make commands easier to copy

bab2d20

Fix typos and other minor things

aecd409

ghost assigned jessebrennan Jul 16, 2018

jessebrennan approved these changes Jul 16, 2018

View reviewed changes

mikebaumann suggested changes Jul 17, 2018

View reviewed changes

Fixed More Mistakes in Docs

b78b3fc

mikebaumann approved these changes Jul 17, 2018

View reviewed changes

		@@ -1,93 +1,177 @@
		# cgp-deployment
		# cgp-deployment (Commons Edition)

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