Update Readme and docs

README.md

@@ -2,34 +2,85 @@
 
 [![Build
 Status](https://git.biohpc.swmed.edu/BioHPC/astrocyte_example_wordcount/badges/master/build.svg)](https://git.biohpc.swmed.edu/BioHPC/astrocyte_example_wordcount/commits/master)
-[![Astrocyte](https://img.shields.io/badge/astrocyte-%E2%89%A50.1.0-blue.svg)](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html)
+[![Astrocyte](https://img.shields.io/badge/astrocyte-%E2%89%A52.0.0-blue.svg)](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html)
 
-This is an example workflow package for astrocyte. It contains a worfklow
-to count the occurences of each word in a text file.
+This is an example workflow package for astrocyte. It contains a workflow to count the occurrences of each word
+in a text file.
 
 ## The Workflow
 
 The workflow `workflow/main.nf` has three processes:
 
-  - Convert all the text in the input files to uppercase
-  - Split the text so each word is on a separate line
-  - Sort, find and count the occurence of unique words
+- Convert all the text in the input files to uppercase
+- Split the text so each word is on a separate line
+- Sort, find and count the occurrence of unique words
+
+This example uses SLURM to finish the calculation tasks. It may be slow due to the workload of the SLURM on BioHPC.
 
 ## Parameters
 
-There is a single parameter `story`. This provides 1 or more files that the
-workflow should run on.
+There is a single parameter `story`. This provides 1 or more files that the workflow should run on.
+
+## Example Usage
+
+Check the workflow package and Astrocyte configurations.
+
+```bash
+module load astrocyte/2.0.0
+astrocyte_cli check astrocyte_example_wordcount
+```
+
+Test run this workflow package with default parameters
+
+```bash
+astrocyte_cli test astrocyte_example_wordcount
+```
+
+Run this workflow package with default parameters
+
+```bash
+astrocyte_cli run astrocyte_example_wordcount
+```
+
+Run this workflow package with your own txt file (e.g. `mobydick-1.txt`)
+
+```bash
+astrocyte_cli run astrocyte_example_wordcount --param="story,mobydick-1.txt"
+```
+
+Prepare the containers and libraries for Vizapp.
+
+```bash
+astrocyte_cli viz-prepare astrocyte_example_wordcount
+```
+
+Run Vizapp
+
+```bash
+astrocyte_cli viz astrocyte_example_wordcount
+# Go to http://127.0.0.1:8123 in your browser to access the vizapp
+# Use `Ctrl-C` to terminate the R shiny server once finished
+```
 
 ## Containers
+
 ### Astrocyte workflow containers
 
-The `workflow_containers` section in `astrocyte_pkg.yml` defines the URL of the contianers used by this workflow. When the `astrocyte_cli` run this workflow, it will pull the images in this section and save them to `workflow/images/singularity/` for later use.  
-In the workflow, the default configuration located in `workflow/configs/biohpc.config` defines how the Nextflow command to use the singularity executor for the uppercase, toLines, and wordcount processes.
+The `workflow_containers` section in `astrocyte_pkg.yml` defines the URL of the containers used by this workflow.
+When the `astrocyte_cli` run this workflow, it will pull the images in this section and save them to
+`workflow/images/singularity/` for later use. In the workflow, the default configuration located in
+`workflow/configs/biohpc.config` defines how the Nextflow command to use the singularity executor for the uppercase,
+toLines, and word count processes.
 
 ### Vizapp containers
 
-The `astrocyte_cli` version 2.0.0 supports containerized vizapp, so that vizapp becomes more independent and can be run on multiple platforms. The astrocyte workflow developers do not need to change their `vizapp_*` settings in `astrocyte_pkg.yml` to use this feature. The `shiny-prepare` command with the `--with-container` option will pull the right version of `R` container from the BioHPC "[Astrocyte Container Images](https://git.biohpc.swmed.edu/biohpc/astrocyte-container-images)" registry and save it to the `vizapp` folder for later use. Also, it will create a folder `vizapp/.rlibrary` to install the dependencies pacages.
-
+The `astrocyte_cli` version 2.0.0 supports containerized vizapp, so that vizapp becomes more independent
+and can be run on multiple platforms. The astrocyte workflow developers do not need to change their `vizapp_*`
+settings in `astrocyte_pkg.yml` to use this feature. The `viz-prepare` command with the `--with-container` option
+will pull the right version of `R` container from the BioHPC
+"[Astrocyte Container Images](https://git.biohpc.swmed.edu/biohpc/astrocyte-container-images)" registry and save it
+to the `vizapp` folder for later use. Also, it will create a folder `vizapp/.rlibrary` to install the dependencies
+packages.
 
 ## Questions
 

docs/index.md

 # Example Wordcount Package
 
-This is an example workflow package for astrocyte. It contains a worfklow
-to count the occurences of each word in a text file.
+This is an example workflow package for astrocyte. It contains a workflow to count the occurrences of each word
+in a text file.
 
 ## The Workflow
 
 The workflow `workflow/main.nf` has three processes:
 
-  - Convert all the text in the input files to uppercase
-  - Split the text so each word is on a separate line
-  - Sort, find and count the occurence of unique words
+- Convert all the text in the input files to uppercase
+- Split the text so each word is on a separate line
+- Sort, find and count the occurrence of unique words
+
+This example uses SLURM to finish the calculation tasks. It may be slow due to the workload of the SLURM on BioHPC.
 
 ## Parameters
 
-There is a single parameter `story`. This provides 1 or more files that the
-workflow should run on.
+There is a single parameter `story`. This provides 1 or more files that the workflow should run on.
+
+## Example Usage
+
+Check the workflow package and Astrocyte configurations.
+
+```bash
+module load astrocyte/2.0.0
+astrocyte_cli check astrocyte_example_wordcount
+```
+
+Test run this workflow package with default parameters
+
+```bash
+astrocyte_cli test astrocyte_example_wordcount
+```
+
+Run this workflow package with default parameters
+
+```bash
+astrocyte_cli run astrocyte_example_wordcount
+```
+
+Run this workflow package with your own txt file (e.g. `mobydick-1.txt`)
+
+```bash
+astrocyte_cli run astrocyte_example_wordcount --param="story,mobydick-1.txt"
+```
+
+Prepare the containers and libraries for Vizapp.
+
+```bash
+astrocyte_cli viz-prepare astrocyte_example_wordcount
+```
+
+Run Vizapp
+
+```bash
+astrocyte_cli viz astrocyte_example_wordcount
+# Go to http://127.0.0.1:8123 in your browser to access the vizapp
+# Use `Ctrl-C` to terminate the R shiny server once finished
+```
+
+## Containers
+
+### Astrocyte workflow containers
+
+The `workflow_containers` section in `astrocyte_pkg.yml` defines the URL of the containers used by this workflow.
+When the `astrocyte_cli` run this workflow, it will pull the images in this section and save them to
+`workflow/images/singularity/` for later use. In the workflow, the default configuration located in
+`workflow/configs/biohpc.config` defines how the Nextflow command to use the singularity executor for the uppercase,
+toLines, and word count processes.
+
+### Vizapp containers
+
+The `astrocyte_cli` version 2.0.0 supports containerized vizapp, so that vizapp becomes more independent
+and can be run on multiple platforms. The astrocyte workflow developers do not need to change their `vizapp_*`
+settings in `astrocyte_pkg.yml` to use this feature. The `viz-prepare` command with the `--with-container` option
+will pull the right version of `R` container from the BioHPC
+"[Astrocyte Container Images](https://git.biohpc.swmed.edu/biohpc/astrocyte-container-images)" registry and save it
+to the `vizapp` folder for later use. Also, it will create a folder `vizapp/.rlibrary` to install the dependencies
+packages.
 
 ## Questions
 
 If you have any questions about this workflow example, or Astrocyte in general,
 please contact the BioHPC team via biohpc-help@utsouthwestern.edu
 
-
 ![BioHPC Logo](https://git.biohpc.swmed.edu/biohpc/astrocyte_example_wordcount/raw/master/docs/biohpc_logo_100pxh.png "BioHPC Logo")