Merge pull request #12 from SD2E/devel

selectively editing out references to singularity in the create_app p…

Author: wjallen

docs/create_app.md

@@ -13,7 +13,7 @@ looking for is not available? Using the Agave CLI, you can create your own.
 
 The essential components you need to create your own app are:
 
-1. A Docker or Singularity image containing the executable and all runtime dependencies
+1. A Docker image containing the executable and all runtime dependencies
 2. A wrapper script (generally written in bash) that runs the executable
 3. A test script (also written in bash) for testing the executable outside of the Agave environment
 

docs/create_app_02.md

@@ -12,9 +12,7 @@ on hubs such as
 
 This tutorial is a quick and dirty summary of how to build your own Docker image
 as if there is not one available for your executable. This is not meant to replace
-the full [Docker documentation](https://docs.docker.com/develop/). Please note
-that [Singularity images](http://singularity.lbl.gov/docs-hpc) are also amenable
-to this infrastructure.
+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).
@@ -150,8 +148,7 @@ Once built, test the new image with an example command:
 ```
 
 *Note: Calling the complete path to executables is sometimes safer than relying
-on PATH environment variables, especially when translating between Docker and
-Singularity*
+on PATH environment variables*
 
 If you see the FastQC help text, the installation likely was successful.
 At this time, it might be prudent to set up a test with real data as well. The

docs/create_app_03.md

@@ -85,8 +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. It is written in this
-way to be flexible and compatible to both Docker and Singularity.
+(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,