reorganizing agave apps part

Author: wjallen

docs/01.install_cli.md

@@ -1,13 +1,15 @@
 ---
 layout: page
-title: Install and Configure the CLI
+title: Install and Configure the SD2E CLI
 tagline:
 ---
 
 The primary method for interacting with the SD2E platform is the
 [SD2E command line interface (CLI)](https://github.com/SD2E/sd2e-cli).
-The CLI is a collection of ~150 shell scripts and other resources for managing
-authorization, files, systems, applications, jobs, and more.
+The SD2E CLI is a collection of several other CLIs including Agave, Abaco,
+TACCLab, and TACCReg. In total, they comprise  ~150 shell scripts and other
+resources for managing authorization, files, systems, applications, jobs, and
+more.
 
 There are three methods to install the CLI, choose whichever fits your preferred
 working environment:

docs/02.modify_systems.md

@@ -1,6 +1,6 @@
 ---
 layout: page
-title: Modify Existing Systems
+title: Modify an Existing System
 tagline:
 ---
 

docs/03.apps_init.md

@@ -0,0 +1,34 @@
+---
+layout: page
+title: Title Here
+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.modify_applications.md docs/03.modify_app.mddocs/03.modify_applications.md renamed to docs/03.modify_app.md

@@ -1,69 +1,20 @@
 ---
 layout: page
-title: Modify Existing Systems and Applications
+title: Modify an Existing Application
 tagline:
 ---
 
-Agave [systems](02.create_systems.md) and [apps](03.create_app.md) are described by
-`json` files and added to the SD2E tenant using the command line interface. To
-modify a system or app after it has been added, simply edit the original `json`
-file and use the command line interface to push the changes to the SD2E tenant.
+Agave [apps](03.old_create_app.md) are described by `json` files and added to the
+SD2E tenant using the command line interface. To modify an  app after it has
+been added, simply edit the original `json` file and use the command line
+interface to push the changes to the SD2E tenant.
 
-Common examples are shown below.
-
-
-<br>
-#### Modify an Agave system
-
-This is an example Agave storage system `json` file from an
-[earlier section](create_systems.md) of this user guide:
-```
-{
-  "id": "jetstream-storage-username",
-  "name": "My Jetstream Storage System",
-  "description": "My system for storing data on jetstream instance 129.114.104.39",
-  "status": "UP",
-  "type": "STORAGE",
-  "storage": {
-    "host": "129.114.104.39",
-    "port": 22,
-    "protocol": "SFTP",
-    "rootDir": "/home/username",
-    "homeDir": "/",
-    "auth": {
-      "publicKey": " <enter public key here> ",
-      "privateKey": " <enter private key here> ",
-      "username": "username",
-      "type": "SSHKEYS"
-    }
-  }
-}
-```
-
-This storage system is attached to a [Jetstream instance](https://jetstream-cloud.org/).
-Users of this and other cloud environments know that IP addresses for instances may
-change. If your Jetstream instance IP address changes, there is no need to delete the old
-storage system and create a new one. Instead, you can modify the existing storage system
-to use the new IP address.
-
-Edit the original system `json` file to reflect the new IP address (in the case above,
-the `description` and `host` fields would need to be edited. Then, perform the
-following:
-```
-% systems-addupdate -F jetstream-storage-username.json jetstream-storage-username
-```
-
-To confirm that the changes have taken place, verbosely list the contents of the
-storage system:
-```
-% systems-list -v jetstream-storage-username
-```
 
 <br>
 #### Modify an Agave app
 
-This is an example Agave app `json` file from an
-[earlier section](create_app_04.md) of this user guide:
+This is an example Agave app `json` file from
+[another section](03.old_create_app_04.md) of this user guide:
 ```
 {
   "name": "fastqc-username",
@@ -106,11 +57,11 @@ This is an example Agave app `json` file from an
 ```
 
 If a new version of FastQC was released (e.g. 0.11.6), that would be cause to
-[create a new app](create_app.md), using this current app as a template. An
-example case where it would be approriate to modify an existing app is,
-for example, to a default file for the `fastq` input.
+[create a new app](03.old_create_app.md), using this current app as a template.
+A case where it would be appropriate to modify an existing app is, for example,
+to add a default file for the `fastq` input.
 
-If you followed the [Create Custom Applications](create_app.md) user guide,
+If you followed the [Create Custom Applications](03.old_create_app.md) user guide,
 then you may have a sample fastq file located here:
 
 `agave://data-tacc-work-username/sd2e-data/sample/SP1.fq`
@@ -157,7 +108,7 @@ you may consider disabling the earlier app. The following command toggles the
 <br>
 #### Further help
 
-Additional system and app `json` fields can be found in in the online
+Additional app `json` fields can be found in in the online
 [Agave documentation](http://developer.tacc.cloud/).
 
 

docs/create_app.md docs/03.old_create_app.mddocs/create_app.md renamed to docs/03.old_create_app.md

@@ -4,11 +4,14 @@ title: Create Custom Applications
 tagline:
 ---
 
+##### *NOTE: This build process works, but has been streamlined in a different guide. Please refer to the new page for [Creating Apps](03.apps_init.md). The old instructions will be kept below for reference.*
+
+<br><br><br>
 You can find Agave applications ("apps") in the SD2E catalog by using the `apps-list`
-command described [previously](find_application.md). What if the app you are
+command described [previously](02.find_application.md). What if the app you are
 looking for is not available? Using the Agave CLI, you can create your own.
 
-<br> 
+<br>
 #### Components of an app
 
 The essential components you need to create your own app are:
@@ -18,21 +21,21 @@ The essential components you need to create your own app are:
 3. A test script (also written in bash) for testing the executable outside of the Agave environment
 
 Several example apps exist and all components are visible. For example, visit the
-[SD2E Docker hub](https://hub.docker.com/u/sd2e/) to view existing app containers.
+[SD2E Docker Hub](https://hub.docker.com/u/sd2e/) to view existing app containers.
 And, example app bundles can be viewed on the
-[SD2E github page](https://github.com/SD2E/reactors-etl/tree/master/reactors).
+[SD2E GitHub page](https://github.com/SD2E/reactors-etl/tree/master/reactors).
 
 <br>
 #### Create your own by example
 
-The best way to demonstrate the creation of a custom app is by example. The 
+The best way to demonstrate the creation of a custom app is by example. The
 following sub-pages will go through the process:
 
-1. [Clone an example app](create_app_01.md)
-2. [Containerize your executable](create_app_02.md)
-3. [Build wrapper and test scripts](create_app_03.md)
-4. [Add your app to the SD2E tenant](create_app_04.md)
-5. [Best practices and next steps](create_app_05.md)
+1. [Clone an example app](03.old_create_app_01.md)
+2. [Containerize your executable](03.old_create_app_02.md)
+3. [Build wrapper and test scripts](03.old_create_app_03.md)
+4. [Add your app to the SD2E tenant](03.old_create_app_04.md)
+5. [Best practices and next steps](03.old_create_app_05.md)
 
 
 ---

docs/create_app_01.md docs/03.old_create_app_01.mddocs/create_app_01.md renamed to docs/03.old_create_app_01.md

@@ -14,7 +14,7 @@ inputs and outputs, what flags might be used, etc.).
 
 *Prerequisite: `git` should be installed on your local machine*
 
-On the [SD2E github pages](https://github.com/SD2E/reactors-etl),
+On the [SD2E GitHub pages](https://github.com/SD2E/reactors-etl),
 you will find examples of several apps that have already
 been built. Clone the entire repo using git and navigate into the `reactors` folder:
 ```
@@ -34,11 +34,11 @@ fcs-tasbe-tacc/         kallisto/               msf/
 ```
 
 As of this writing, there are seven example apps including `hello-container`,
-which is both a simple example app and a template for creating new apps. Spend 
+which is both a simple example app and a template for creating new apps. Spend
 some time navigating through the folders to get an idea of what components are
 part of an app bundle.
 
-<br> 
+<br>
 #### Structure of an app
 
 The basic structure of an app looks as follows:
@@ -60,12 +60,12 @@ hello-container/
 ```
 
 At the top level, you will find a `Dockerfile` and `build.sh` script. These are
-necessary for building the container reproducibly, and having them will facilitate 
+necessary for building the container reproducibly, and having them will facilitate
 future app updates. The `deploy.sh` script is the final script of the app building
 process which helps the user add their app to the Agave SD2E tenant.
 
 The major subdirectory is named `hello-container-0.1.0/` - a concatenation of the
-name of the app and the version of the executable. This directory contains both 
+name of the app and the version of the executable. This directory contains both
 `runner-template.sh`, which is a script directing how the app should be run upon
 invocation, and `tester.sh`, which is a clone of `runner-template.sh` for testing
 locally. Also included are template files `app.json` and `job.json` which contai
@@ -114,8 +114,8 @@ executable.
 
 
 ---
-Proceed to [Containerize your executable](create_app_02.md)
+Proceed to [Containerize your executable](03.old_create_app_02.md)
 
-Go back to [Create Custom Applications](create_app.md)
+Go back to [Create Custom Applications](03.old_create_app.md)
 
 Return to the [API Documentation Overview](../index.md)

docs/create_app_02.md docs/03.old_create_app_02.mddocs/create_app_02.md renamed to docs/03.old_create_app_02.md

@@ -15,12 +15,12 @@ as if there is not one available for your executable. This is not meant to repla
 the full [Docker documentation](https://docs.docker.com/develop/).
 
 We will continue with the example of FastQC from the
-[previous page](create_app_01.md).
+[previous page](03.old_create_app_01.md).
 
 <br>
 #### Choose a source image
 
-*Prerequisite: You should have a [Docker ID](https://hub.docker.com) and 
+*Prerequisite: You should have a [Docker ID](https://hub.docker.com) and
 `docker` should be installed on your local machine*
 
 The only dependency for [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
@@ -92,8 +92,8 @@ to our `src/` directory, then mounted that directory within the image, e.g.:
 % docker run --rm -it -v $PWD:/src sd2e/base:ubuntu16
 ...etc
 ```
-That route is perfectly reasonable and can be followed here. However, some packages 
-have very large zip or tar.gz files (100s of MB), and would be cumbersome to keep 
+That route is perfectly reasonable and can be followed here. However, some packages
+have very large zip or tar.gz files (100s of MB), and would be cumbersome to keep
 in this `fastqc` app bundle folder. It is up to the app developer to find the balance
 between completeness of source files and responsible disk usage.
 
@@ -118,12 +118,12 @@ RUN apt-get update \
     && apt-get upgrade -y \
     && apt-get install wget -y \
     && apt-get install zip -y \
-    && apt-get install default-jre -y 
+    && apt-get install default-jre -y
 
 RUN wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip \
     && unzip fastqc_v0.11.5.zip \
     && rm fastqc_v0.11.5.zip \
-    && chmod +x FastQC/fastqc 
+    && chmod +x FastQC/fastqc
 
 ENV PATH "/FastQC/:$PATH"
 ```
@@ -172,7 +172,7 @@ If successful, you should find the output files `SP1_fastqc.html` and `SP1_fastq
 in the `~/fastqc/example/` directory.
 
 
-<br> 
+<br>
 #### Push your image to the cloud
 
 Finally, push your Docker image to a publicly available repository. It can be
@@ -200,8 +200,8 @@ And execute the script with `bash` to push your image to the cloud:
 Next, we will continue to edit files in the app bundle to call this new image.
 
 ---
-Proceed to [Build wrapper and test scripts](create_app_03.md)
+Proceed to [Build wrapper and test scripts](03.old_create_app_03.md)
 
-Go back to [Create Custom Applications](create_app.md)
+Go back to [Create Custom Applications](03.old_create_app.md)
 
 Return to the [API Documentation Overview](../index.md)

docs/create_app_03.md docs/03.old_create_app_03.mddocs/create_app_03.md renamed to docs/03.old_create_app_03.md

@@ -85,7 +85,7 @@ replace `USERNAME` with your Docker ID (or project space where the image is
 located). Also in the above file, the `container_exec.sh` script is sourced,
 '`perl /FastQC/fastqc`' is the command to execute, and the parameter passed to the
 command is the input fastq file (`${fastq}`). The final command in the script
-(begging with `DEBUG=1`) is the main container run command. 
+(begging with `DEBUG=1`) is the main container run command.
 
 At the bottom of the script are a few template functions that you can develop
 to validate that the test ran correctly. Here,
@@ -106,11 +106,11 @@ generated in the `~/fastqc/example/` folder. (Make sure not to confuse old outpu
 files with new output files - check the time stamps or remove the output and run
 again).
 
-<br> 
+<br>
 #### Write the wrapper script
 
 The file loacted at `~/fastqc/fastqc-0.11.6/runner-template.sh` contains runtime
-instructions for your app in Agave. Essentially, it is a subset of your test 
+instructions for your app in Agave. Essentially, it is a subset of your test
 script. Copy the test script to `runner_template.sh` and retain only the following
 lines:
 ```
@@ -129,8 +129,8 @@ as it will be defined later by Agave. We also do not mount our example data into
 the Docker container, as that will be taken care of in production.
 
 ---
-Proceed to [Add your app to the SD2E tenant](create_app_04.md)
+Proceed to [Add your app to the SD2E tenant](03.old_create_app_04.md)
 
-Go back to [Create Custom Applications](create_app.md)
+Go back to [Create Custom Applications](03.old_create_app.md)
 
 Return to the [API Documentation Overview](../index.md)