fix links in readme

* add-docs: (21 commits)
  clarify gcp kubernetes guide
  add link to blog post to travis docs page
  clarify k8s minikube instructions
  update installation instructions to clarify and mention s3 buckets
  fix readme to match docs index - shorter and more succinct
  update documentation to mark unfinished TBA pages
  add complete and tested gcp instructions
  add shields for minikube, k8s, and ubuntu versions
  update comments in travis file, remove unnecessary redis image init
  add ubuntu shields
  add quickstart section to index
  fix url again
  use https address for submodule, for travis
  add custom css and images dir
  add requirements file for documentation building
  add travis tests page
  update gitignore for mkdocs
  add mkdocs-material-dib submodule
  removing kubernetes md files, moved to docs/
  add fleshed out docs
  ...

README.md

@@ -25,8 +25,8 @@ k8s = kubernetes
 byok8s is a command line utility that launches
 a Snakemake workflow on an existing Kubernetes
 cluster. This allows you to do something
-like this (also see the [Installation](installing.md)
+like this (also see the [Installation](docs/installing.md)
-and [Quickstart](quickstart.md) guides in the
+and [Quickstart](docs/quickstart.md) guides in the
 documentation):
 
 ```
@@ -45,12 +45,8 @@ minikube stop
 ```
 
 ## Getting Up and Running
-Snakemake workflows are provided via a Snakefile by
-the user. Snakemake runs tasks on the Kubernetes (k8s)
-cluster. The approach is for the user to provide
-their own Kubernetes cluster (byok8s = Bring Your
 
-See the [Quickstart Guide](quickstart.md) to get up and 
+See the [Quickstart Guide](docs/quickstart.md) to get up and 
 running with byok8s.
 
 ## How does byok8s work?
@@ -102,11 +98,11 @@ or Google Cloud.
 But the compute nodes can also be virtual, which is where
 [minikube](https://github.com/kubernetes/minikube) comes in.  It creates a
 kubernetes cluster that is entirely local and virtual, which makes testing
-easy. See the [byok8s Minikube Guide](kubernetes_minikube.md) for details
+easy. See the [byok8s Minikube Guide](docs/kubernetes_minikube.md) for details
 about how to use minikube with byok8s.
 
 The Travis CI tests also utilize minikube to run test workflows. See [byok8s
-Travis Tests](travis_tests.md) for more information.
+Travis Tests](docs/travis_tests.md) for more information.
 
 ## Cloud Providers
 
@@ -122,9 +118,8 @@ We have guides for the following:
 
 |  Cloud Provider             | Kubernetes Service              | Guide                                           | State      |
 |-----------------------------|---------------------------------|-------------------------------------------------|------------|
-| Minikube (on AWS EC2)       | Minikube                        | [byok8s Minikube Guide](kubernetes_minikube.md) |   Finished |
+| Minikube (on AWS EC2)       | Minikube                        | [byok8s Minikube Guide](docs/kubernetes_minikube.md) |   Finished |
-| Google Cloud Platform (GCP) | Google Container Engine (GKE)   | [byok8s GCP GKE Guide](kubernetes_gcp.md)       |   Finished |
+| Google Cloud Platform (GCP) | Google Container Engine (GKE)   | [byok8s GCP GKE Guide](docs/kubernetes_gcp.md)       |   Finished |
-| Amazon Web Services (AWS)   | Elastic Container Service (EKS) | [byok8s AWS EKS Guide](kubernetes_aws.md)       | Unfinished |
+| Amazon Web Services (AWS)   | Elastic Container Service (EKS) | [byok8s AWS EKS Guide](docs/kubernetes_aws.md)       | Unfinished |
-| Digital Ocean (DO)          | DO Kubernetes (DOK)             | [byok8s DO DOK Guide](kubernetes_dok.md)        | Unfinished |
+| Digital Ocean (DO)          | DO Kubernetes (DOK)             | [byok8s DO DOK Guide](docs/kubernetes_dok.md)        | Unfinished |
 
-Own Kubernetes).

docs/installing.md

@@ -1,26 +1,21 @@
 # Installing byok8s
 
-byok8s requires two pieces of prerequisite software:
+byok8s requires pieces of prerequisite software:
 
 - python (conda)
 - virtualenv (optional)
 
-It also requires an AWS S3 bucket to be specified 
-(the bucket must exist and credentials to access it
-must be provided via environment variables, see the
-[Quickstart](quickstart.md)).
-
 Additionally, if you are planning to run byok8s on
 a local virtual kubernetes cluster, you must install:
 
 - minikube
 
-Otherwise, if you are planning on running byok8s on 
+Otherwise, if you are planning on running byok8s on remote 
-remote kubernetes clusters provided by cloud providers, 
+kubernetes clusters provided by cloud providers
-you must install:
+or etc., you must install:
 
 - kubernetes, ***OR***
-- a cloud provider command line tool (`gcloud`, `aws`)
+- a cloud provider command line tool (`gcloud`, `aws`) 
 
 ## Installing Python
 

docs/kubernetes_gcp.md

@@ -40,9 +40,9 @@ utility will let you know if it needs APIs enabled for actions.  If it can't
 enable the API for you, it will give you a direct link to the relevant Google
 Cloud Console page.
 
-## Google Kubernetes Engine
+## Google Kubernetes Engine (GKE)
 
-GKE uses Google Cloud compute nodes to run a kubernetes cluster
+GKE uses GCP compute nodes to run a kubernetes cluster
 on Google Cloud infrastructure. It automatically sets up the
 cluster for you, and allows you to use `kubectl` and `gcloud` to
 manage and interact with the remote cluster.
@@ -255,6 +255,9 @@ Events:
   Normal  Started                6s    kubelet, gke-mycluster-default-pool-b44fa389-vh3x  Started container
 ```
 
+Congratulations! You've successfully run an executable Snakemake workflow
+on a Google Cloud kubernetes cluster!
+
 Delete the GKE cluster when you are done:
 
 ```

docs/kubernetes_minikube.md

@@ -81,13 +81,14 @@ To fix the problem with the DNS settings, we have to patch
 the CoreDNS image being used by `kube-system`.
 To do that, use the file
 [`test/fixcoredns.yml`](https://github.com/charlesreid1/2019-snakemake-byok8s/blob/master/test/fixcoredns.yml)
+[`test/fixcoredns.yml`](https://github.com/charlesreid1/2019-snakemake-byok8s/blob/master/test/fixcoredns.yml)
 in this repository with `kubectl apply`:
 
 ```plain
 # Fix the DNS container
 kubectl apply -f fixcoredns.yml
 
-# Delete all kube-system containers
+# Delete all kube-system containers 
 kubectl delete --all pods --namespace kube-system
 ```
 
@@ -110,6 +111,6 @@ export AWS_SECRET_ACCESS_KEY="XXXXX"
 byok8s workflow-alpha params-blue --s3-bucket=mah-bukkit 
 ```
 
-Congratulations! You've just run an executable Snakemake workflow
+Congratulations! You've just run an executable Snakemake workflow 
-on a minikube kubernetes cluster.
+on a minikube kubernetes cluster.