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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
......
# 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")
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