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Fix formatting
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@cansavvy
cansavvy authored Dec 3, 2024
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52 changes: 26 additions & 26 deletions 03-using-containers.qmd
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Expand Up @@ -22,18 +22,18 @@ xaringanExtra::style_panelset_tabs(font_family = "inherit")
## Activity Instructions {.panelset}
### Docker
#### Set up
<input type="checkbox"> Go here to [install Docker](https://www.docker.com/get-started), following the instructions for your particular operating system.
<input type="checkbox"> If you don't have a Docker account create an account when prompted, or [go here](https://hub.docker.com/).
<input type="checkbox"> After you install Docker, start up Docker desktop by double clicking on the app. It may take some time to start up.
<input type="checkbox"> Go here to [install Docker](https://www.docker.com/get-started), following the instructions for your particular operating system.
<input type="checkbox"> If you don't have a Docker account create an account when prompted, or [go here](https://hub.docker.com/).
<input type="checkbox"> After you install Docker, start up Docker desktop by double clicking on the app. It may take some time to start up.

```{r, out.width = "100%", echo = FALSE}
ottrpal::include_slide("https://docs.google.com/presentation/d/1T5Lfei2UVou9b0qaUCrWXmkcIwAao-UcN4pHMPEE4CY/edit#slide=id.g30a4ed49e59_0_686")
```

#### Get workshop files
<input type="checkbox"> Download the files for this activity clicking here: https://github.com/fhdsl/containers-for-scientists-sandbox/archive/refs/heads/main.zip
<input type="checkbox"> Put this file on your desktop so it is easily findable.
<input type="checkbox"> Double click the zip file (or right click and choose "unzip" or "decompress" to unzip the file.
<input type="checkbox"> Download the files for this activity clicking here: https://github.com/fhdsl/containers-for-scientists-sandbox/archive/refs/heads/main.zip
<input type="checkbox"> Put this file on your desktop so it is easily findable.
<input type="checkbox"> Double click the zip file (or right click and choose "unzip" or "decompress" to unzip the file.

```{r, out.width = "100%", echo = FALSE}
ottrpal::include_slide("https://docs.google.com/presentation/d/1T5Lfei2UVou9b0qaUCrWXmkcIwAao-UcN4pHMPEE4CY/edit#slide=id.g30a4ed49e59_0_693")
Expand Down Expand Up @@ -79,8 +79,8 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1T5Lfei2UVou9b0qa

##### Step 2: Check what images you have

<input type="checkbox"> To see what images we have we can run `docker image ls`.
<input type="checkbox"> We should see `cansav09/practice-image:1` show up in the output.
<input type="checkbox"> To see what images we have we can run `docker image ls`.
<input type="checkbox"> We should see `cansav09/practice-image:1` show up in the output.

```{r, out.width = "100%", echo = FALSE}
ottrpal::include_slide("https://docs.google.com/presentation/d/1T5Lfei2UVou9b0qaUCrWXmkcIwAao-UcN4pHMPEE4CY/edit#slide=id.g30a4ed49e59_0_752")
Expand All @@ -94,7 +94,7 @@ Remember images can be shared easily but to actually use the stuff we need to tu
ottrpal::include_slide("https://docs.google.com/presentation/d/1T5Lfei2UVou9b0qaUCrWXmkcIwAao-UcN4pHMPEE4CY/edit#slide=id.g30a4ed49e59_0_760")
```

<input type="checkbox"> To launch the image for use, we can use `docker run` to turn it into a **container**.
<input type="checkbox"> To launch the image for use, we can use `docker run` to turn it into a **container**.
```
docker run cansav09/practice-image:1
```
Expand Down Expand Up @@ -124,7 +124,7 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1T5Lfei2UVou9b0qa

##### Step 4: Run a single command

<input type="checkbox"> To run stuff interactively from the command line we can do:
<input type="checkbox"> To run stuff interactively from the command line we can do:

```
docker exec -it <PUT_CONTAINER_ID_HERE> bash
Expand Down Expand Up @@ -156,12 +156,12 @@ dev init lib64 media proc run sys var
root@e7b19cfb4461:/#
```

<input type="checkbox"> When you are ready to leave your container type `exit` and press Enter.
<input type="checkbox"> When you are ready to leave your container type `exit` and press Enter.


##### Step 5: Try calling a script

<input type="checkbox"> To run a script using the docker container we could just add reference to a script at the end:
<input type="checkbox"> To run a script using the docker container we could just add reference to a script at the end:

```
docker exec -it <PUT_CONTAINER_ID_HERE> bash run_analysis.sh
Expand All @@ -188,18 +188,18 @@ This won't work because the file `run_analysis.sh` is not a file that our contai

### Podman
#### Set up Podman
<input type="checkbox"> Go here to [install Podman](https://podman.io/docs/installation), following the instructions for your particular operating system.
<input type="checkbox"> Open up your [command line](https://towardsdatascience.com/a-quick-guide-to-using-command-line-terminal-96815b97b955).
<input type="checkbox"> Start up Podman by running the following:
<input type="checkbox"> Go here to [install Podman](https://podman.io/docs/installation), following the instructions for your particular operating system.
<input type="checkbox"> Open up your [command line](https://towardsdatascience.com/a-quick-guide-to-using-command-line-terminal-96815b97b955).
<input type="checkbox"> Start up Podman by running the following:
```
podman machine init
podman machine start
```

#### Get workshop files
<input type="checkbox"> Download the files for this activity clicking here: https://github.com/fhdsl/containers-for-scientists-sandbox/archive/refs/heads/main.zip
<input type="checkbox"> Put this file on your desktop so it is easily findable.
<input type="checkbox"> Double click the zip file (or right click and choose "unzip" or "decompress" to unzip the file.
<input type="checkbox"> Download the files for this activity clicking here: https://github.com/fhdsl/containers-for-scientists-sandbox/archive/refs/heads/main.zip
<input type="checkbox"> Put this file on your desktop so it is easily findable.
<input type="checkbox"> Double click the zip file (or right click and choose "unzip" or "decompress" to unzip the file.

```{r, out.width = "100%", echo = FALSE}
ottrpal::include_slide("https://docs.google.com/presentation/d/1T5Lfei2UVou9b0qaUCrWXmkcIwAao-UcN4pHMPEE4CY/edit#slide=id.g30a4ed49e59_0_693")
Expand Down Expand Up @@ -229,7 +229,7 @@ Pulling is a term used in GitHub terminology too. It just means we're taking som
ottrpal::include_slide("https://docs.google.com/presentation/d/1T5Lfei2UVou9b0qaUCrWXmkcIwAao-UcN4pHMPEE4CY/edit#slide=id.g30a4ed49e59_0_732")
```

<input type="checkbox"> Run this command in your Terminal or Command Prompt window:
<input type="checkbox"> Run this command in your Terminal or Command Prompt window:

```
podman pull cansav09/practice-image:1
Expand All @@ -243,8 +243,8 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1T5Lfei2UVou9b0qa

##### Step 2: Check what images you have

<input type="checkbox"> To see what images we have we can run `podman image ls`.
<input type="checkbox"> You should see `cansav09/practice-image:1` show up in the output and it will look a bit like this below:
<input type="checkbox"> To see what images we have we can run `podman image ls`.
<input type="checkbox"> You should see `cansav09/practice-image:1` show up in the output and it will look a bit like this below:

```
docker.io/cansav09/practice-image 1 91619ca583b8 1 month ago 2.39 GB
Expand All @@ -258,7 +258,7 @@ Remember images can be shared easily but to actually use the stuff we need to tu
ottrpal::include_slide("https://docs.google.com/presentation/d/1T5Lfei2UVou9b0qaUCrWXmkcIwAao-UcN4pHMPEE4CY/edit#slide=id.g30a4ed49e59_0_760")
```

<input type="checkbox"> To launch the image for use, we can use `podman run` to turn it into a **container**.
<input type="checkbox"> To launch the image for use, we can use `podman run` to turn it into a **container**.

```
podman run cansav09/practice-image:1
Expand All @@ -272,7 +272,7 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1T5Lfei2UVou9b0qa

Don't worry too much about all this output, every image is configured differently and this output will change depending on that.

<input type="checkbox"> To see what containers we have running we have we can run:
<input type="checkbox"> To see what containers we have running we have we can run:

```
podman ps
Expand Down Expand Up @@ -300,7 +300,7 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1T5Lfei2UVou9b0qa

##### Step 4: Run the container interactively

<input type="checkbox"> To run stuff interactively from the command line we can do:
<input type="checkbox"> To run stuff interactively from the command line we can do:

But you'll need to replace the `<PUT_CONTAINER_ID_HERE>` portion of this command with the `CONTAINER ID` reported when you ran `podman ps`.
```
Expand Down Expand Up @@ -328,12 +328,12 @@ dev init lib64 media proc run sys var
root@e7b19cfb4461:/#
```

<input type="checkbox"> When you are ready to leave your container type `exit` and press Enter.
<input type="checkbox"> When you are ready to leave your container type `exit` and press Enter.


##### Step 5: Try calling a script

<input type="checkbox"> To run a script using the container we could just add reference to a script at the end:
<input type="checkbox"> To run a script using the container we could just add reference to a script at the end:

```
podman exec -it <PUT_CONTAINER_ID_HERE> bash run_analysis.sh
Expand Down

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