stubbing out new app building process

Author: wjallen

docs/03.apps_ci_jenkins.md

@@ -0,0 +1,34 @@
+---
+layout: page
+title: Continuous Integration with Jenkins
+tagline:
+---
+
+Intro text.
+
+1. List element 1
+2. List element 2
+3. List element 3
+
+
+<br>
+#### Header 1
+
+```
+% code block
+```
+
+
+<br>
+#### Header 2
+
+[Example link](https://url/) 
+
+
+<br>
+#### Header 3
+
+
+
+---
+Return to the [API Documentation Overview](../index.md)

docs/03.apps_deploy.md

@@ -0,0 +1,34 @@
+---
+layout: page
+title: "Deploy a Custom Application"
+tagline: Apps-Deploy
+---
+
+Intro text.
+
+1. List element 1
+2. List element 2
+3. List element 3
+
+
+<br>
+#### Header 1
+
+```
+% code block
+```
+
+
+<br>
+#### Header 2
+
+[Example link](https://url/)
+
+
+<br>
+#### Header 3
+
+
+
+---
+Return to the [API Documentation Overview](../index.md)

docs/03.apps_init.md

@@ -1,7 +1,7 @@
 ---
 layout: page
-title: Title Here
-tagline:
+title: "Create a Custom Application"
+tagline: Apps-Init
 ---
 
 Intro text.
@@ -22,7 +22,7 @@ Intro text.
 <br>
 #### Header 2
 
-[Example link](https://url/) 
+[Example link](https://url/)
 
 
 <br>

docs/singularity_gpu_01.md renamed to docs/05.container_gpu.md

@@ -1,12 +1,13 @@
 ---
 layout: page
-title: Utilizing GPUs with Singularity
+title: Run Containers on GPUs
 tagline:
 ---
 
 Utilizing GPGPUs on the Maverick supercomputer through containerized environments.
 
-## Choosing the Right System
+<br>
+#### Choosing the Right System
 
 You can register your app to ANY system at TACC, but Maverick may not always be the best choice if you don't always need GPUs.
 
@@ -19,18 +20,19 @@ You can register your app to ANY system at TACC, but Maverick may not always be
 | Wrangler   | 24         | SSD Filesystem for fast I/O, Hosted Databases, Hadoop, HDFS | Low node-count           |
 | Jetstream  | 24         | Long running instances, root access       | Limited storage                            |
 | Maverick   | 20         | GPUs, high memory nodes                   | Deprecated software stack                 |
-| Chameleon  | Variable   | GPUs, bare metal VM, software defined networking | Difficult to configure              | 
+| Chameleon  | Variable   | GPUs, bare metal VM, software defined networking | Difficult to configure              |
 | Catapult   | 16         | FPGAs                                     | Windows-only                               |
 
 You can learn about all choices at the [TACC Systems Overview](https://www.tacc.utexas.edu/systems/overview). Detailed specifications can be found in the *User Guide* of each system.
 
 If you have an application already configured on a non-tacc system, you can register that system to the SD2E agave tenant.
 
-- [System Registration Guide](https://sd2e.github.io/api-user-guide/docs/create_systems.html)
+- [System Registration Guide](02.create_systems.html)
 
 After registration, you can not only run applications, but access data as well. Just remember that applications will run as YOUR user when you share them with others.
 
-## Containers @ TACC
+<br>
+#### Containers @ TACC
 
 TACC supports containerized compute environments through [Singularity](http://singularity.lbl.gov/), which provides environment encapsulation without privilege escalation (root). Singularity provides the following functionality:
 
@@ -46,7 +48,8 @@ TACC supports containerized compute environments through [Singularity](http://si
 
 Since version 2.3, Singularity has supported the two following workflows
 
-### Local Container Development
+<br>
+##### Local Container Development
 
 Create a Singularity container from scratch.
 
@@ -58,7 +61,8 @@ Create a Singularity container from scratch.
 
 <http://singularity.lbl.gov/archive/docs/v2-3/bootstrap-image>
 
-### Docker Import
+<br>
+##### Docker Import
 
 Utilize your knowledge of Docker to create Singularity images.
 
@@ -67,15 +71,17 @@ Utilize your knowledge of Docker to create Singularity images.
 
 <http://singularity.lbl.gov/archive/docs/v2-3/docs-docker>
 
-### Running the container
+<br>
+##### Running the container
 
 These containers are run without root, so you simply
 
 - run - Run the default functionality of the container, which takes in arguments
 - exec - Execute a specific command inside the container, and then exit
 - shell - Enter the container and interactively run commands
 
-## GPU containers
+<br>
+#### GPU containers
 
 Since Singularity supported docker containers, it has been fairly simple to utilize GPUs for machine learning code like [TensorFlow](https://www.tensorflow.org/). From Maverick, which is TACC's GPU system:
 
@@ -86,7 +92,7 @@ idev -m 60
 module load tacc-singularity
 # Pull your image
 singularity pull docker://nvidia/caffe:latest
-# 
+#
 singularity exec --nv caffe-latest.img caffe device_query -gpu 0
 ```
 
@@ -113,6 +119,11 @@ You probably noticed that we check out the models repository into your `$HOME` d
 
 You may be thinking "what about overlayfs??". The Linux kernel on Maverick does not support overlayfs, so it had to be disabled in our singularity install.
 
-## Build your APP
+<br>
+#### Build your APP
 
-You can then use these methods in your [next Agave app](create_app.md).
+You can then use these methods in your [next Agave app](03.old_create_app.md).
+
+
+---
+Return to the [API Documentation Overview](../index.md)

index.md

@@ -45,15 +45,15 @@ the SD2E platform. Documentation for getting started with the SD2E API is below.
 
   **3 Agave Applications**
 
-    3.1 Create Custom Applications: Apps-Init (*coming soon*)
+    3.1 [Create a Custom Application: Apps-Init](docs/03.apps_init.md)
 
-    3.2 Deploy Custom Applications: Apps-Deploy (*coming soon*)
+    3.2 [Deploy a Custom Application: Apps-Deploy](docs/03.apps_deploy.md)
 
     3.3 [Share an Application with Others](docs/03.share_app.md)
 
     3.4 [Modify an Existing Application](docs/03.modify_app.md)
 
-    3.5 Continuous Integration with Jenkins (*coming soon*)
+    3.5 [Continuous Integration with Jenkins](03.apps_ci_jenkins.md)
 
     3.6 [Old App Building Process](docs/03.old_create_app.md) (*deprecated*)
 
@@ -62,9 +62,9 @@ the SD2E platform. Documentation for getting started with the SD2E API is below.
 
     4.1 Abaco CLI Basics (*coming soon*)
 
-    4.2 Create Custom Reactors: Abaco Init (*coming soon*)
+    4.2 Create a Custom Reactor: Abaco Init (*coming soon*)
 
-    4.3 Deploy Custom Reactors: Abaco Deploy (*coming soon*)
+    4.3 Deploy a Custom Reactor: Abaco Deploy (*coming soon*)
 
     4.4 Share a Reactor with Others (*coming soon*)
 
@@ -81,13 +81,24 @@ the SD2E platform. Documentation for getting started with the SD2E API is below.
 
     5.3 Jupyter Notebooks (*coming soon*)
 
-    5.4 [Singularity GPGPU Containers](docs/singularity_gpu_01.md)
+    5.4 [Run Containers on GPUs](docs/05.container_gpu.md)
 
 
-  **6 Placeholder**
+  **6 Other CLI Tools**
+
+    6.1 TACC Lab CLI (*coming soon*)
+
+    6.2 TACC Registry CLI (*coming soon*)
+
 
   **7 Reference Pages**
 
+    7.1 Base Images (*coming soon*)
+
+    7.2 Applications (*coming soon*)
+
+    7.3 Reactors (*coming soon*)
+
 
 
 <br>