Merge pull request #275 from NBISweden/js-lectures

More lecture updates
NBISweden · Nov 21, 2024 · 97ab1b9 · 97ab1b9
2 parents 43ed0fb + 70c5729
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diff --git a/lectures/conda/conda.qmd b/lectures/conda/conda.qmd
@@ -1,13 +1,11 @@
 ---
 title: 'Managing software environments with <br> <img src="images/conda-logo.png" style="width:50%;padding: 25px 25px 25px 25px;">'
-format: revealjs
+format: 
+  revealjs:
+    mermaid: 
+      theme: neutral
 execute:
   echo: false
-jupyter:
-    kernelspec:
-        display_name: Python 3
-        language: python
-        name: python3
 ---
 
 ## The problem
@@ -19,38 +17,33 @@ _Full reproducibility requires the possibility to recreate the system that was
 originally used to generate the results._
 :::
 
-## Conda is a package, dependency, and environment manager {auto-animate="true"}
+## Conda is a package, dependency, and environment manager
 
 - [package]{.green}: any type of program (_e.g._ multiqc, snakemake etc.)
 
-::: {data-id="flowchart1"}
 ```{mermaid}
 flowchart LR
     multiqc(multiqc)
 ```
-:::
 
-## Conda is a package, dependency, and environment manager {auto-animate="true"}
+## Conda is a package, dependency, and environment manager
 
 - [package]{.green}: any type of program (_e.g._ multiqc, snakemake etc.)
 - [dependency]{.green}: other software required by a package
 
-::: {data-id="flowchart1"}
 ```{mermaid}
 flowchart LR
     multiqc(multiqc) -.-> numpy(numpy)
     multiqc -.-> matplotlib(matplotlib)
     multiqc -.-> python(python)
 ```
-:::
 
-## Conda is a package, dependency, and environment manager {auto-animate="true"}
+## Conda is a package, dependency, and environment manager
 
 - [package]{.green}: any type of program (_e.g._ multiqc, snakemake etc.)
 - [dependency]{.green}: other software required by a package
   - dependencies in turn have their own dependencies
 
-::: {data-id="flowchart1"}
 ```{mermaid}
 flowchart LR
     multiqc(multiqc) -.-> numpy(numpy)
@@ -62,16 +55,14 @@ flowchart LR
     numpy -.-> python
     numpy -.-> libcxx(libcxx)
 ```
-:::
 
-## Conda is a package, dependency, and environment manager {auto-animate="true"}
+## Conda is a package, dependency, and environment manager
 
 - [package]{.green}: any type of program (_e.g._ multiqc, snakemake etc.)
 - [dependency]{.green}: other software required by a package
   - dependencies in turn have their own dependencies
 - [environment]{.green}: a distinct collection of packages
 
-::: {data-id="flowchart1"}
 ```{mermaid}
 flowchart LR
     subgraph environment
@@ -87,13 +78,11 @@ flowchart LR
     numpy -.-> libcxx(libcxx)
     end
 ```
-:::
-
-## Conda channels {auto-animate=true}
 
+## Conda channels
+
 [Channels]{.green} are remote directories containing packages
 
-::: {data-id="m1"}
 ```{mermaid}
 flowchart TD
     ch1[(channel1)] --- p1[package1]
@@ -104,16 +93,15 @@ flowchart TD
     ch2[(channel2)] --- p5[package5]
     ch2[(channel2)] --- p6[package6]
 ```
-:::
 
-## Conda channels {auto-animate=true}
+
+## Conda channels
 
 Two common examples are:
 
 - [bioconda]{.green} (a channel specializing in bioinformatics software)
 - [conda-forge]{.green} (a community-led channel made up of thousands of contributors)
 
-::: {data-id="m1"}
 ```{mermaid}
 flowchart TD
     ch1[(bioconda)] --- p1[bowtie2]
@@ -124,16 +112,14 @@ flowchart TD
     ch2[(conda-forge)] --- p5[jupyter]
     ch2[(conda-forge)] --- p6[wget]
 ```
-:::
 
-## Conda channels {auto-animate=true}
+## Conda channels
 
 Two common examples are:
 
 - [bioconda]{.green} (a channel specializing in bioinformatics software)
 - [conda-forge]{.green} (a community-led channel made up of thousands of contributors)
 
-::: {data-id="m1"}
 ```{mermaid}
 flowchart TD
     ch1[(bioconda)] --- p1[bowtie2]
@@ -147,13 +133,12 @@ flowchart TD
     p5 -.-> l1([conda install -c conda-forge -c bioconda snakemake jupyter])
     p3 -.-> l1
 ```
-:::
 
 ## Defining and sharing environments
 
 Define a Conda environment in an `environment.yml` file:
 
-``` {.yaml code-line-numbers="|1-3|4-12"}
+```{.yaml filename="environment.yml" code-line-numbers="|1-3|4-12"}
 channels:
   - conda-forge
   - bioconda
@@ -168,47 +153,48 @@ dependencies:
   - graphviz=2.38.0
 ```
 
-## Defining and sharing environments {auto-animate="true"}
+## Conda command-line
 
-- Update an existing environment:
+::: {.fragment}
+- Create a new environment:
 
 ```bash
-conda env update -f environment.yml
+conda env create -f environment.yml
 ```
+:::
 
-## Defining and sharing environments {auto-animate="true"}
-
+::: {.fragment}
 - Update an existing environment:
 
 ```bash
 conda env update -f environment.yml
 ```
+:::
 
-- Export environment (including all dependencies) to a file:
-
-```bash
-conda env export > environment.yml
-```
-
-## Defining and sharing environments {auto-animate="true"}
-
+::: {.fragment}
 - Update an existing environment:
 
 ```bash
 conda env update -f environment.yml
 ```
+:::
+
+::: {.fragment}
 
 - Export environment (including all dependencies) to a file:
 
 ```bash
 conda env export > environment.yml
 ```
+:::
 
+::: {.fragment}
 - Export historical environment (only packages explicitly installed):
 
 ```bash
 conda env export --from-history > environment.yml
 ```
+:::
 
 ## Conda, Anaconda, Miniconda, Miniforge...
 

diff --git a/lectures/containers/containers.qmd b/lectures/containers/containers.qmd
@@ -1,8 +1,9 @@
 ---
-title: 'Working with containers
+title: 'Working with containers'
+subtitle: '
         <img src="images/docker-logo.webp" height="130px" style="float:center; padding: 15px 15px 15px 15px;"/>
         <img src="https://apptainer.org/docs/user/main/_static/logo.png" height="130px" style="float:center; padding: 15px 15px 15px 15px;"/>
-        <img src="https://sylabs.io/guides/3.0/user-guide/_static/logo.png" height="130px" style="float:center; padding: 15px 15px 15px 15px;"/>'
+        '
 format: revealjs
 ---
 
@@ -81,14 +82,20 @@ Status: Downloaded image for ubuntu:16.04
 ```
 :::
 
-::: {.fragment}
+## An example: using a different OS
+
+Check OS on local machine
+```{.bash}
+$ uname -a
+Darwin johnsmbp.local 19.6.0 Darwin Kernel Version 19.6.0: [...] x86_64
+```
+
 Run the container interactively and check OS version
 ```{.bash code-line-numbers="|1|2|3"}
 $ docker run -it ubuntu:16.04
 root@407b0fd13fe5:/## uname -a
 Linux 407b0fd13fe5 4.9.60-linuxkit-aufs [...] x86_64 GNU/Linux
 ```
-:::
 
 ## Mounting volumes
 
@@ -168,9 +175,9 @@ docker run \
 ```
 :::
 
-## What is Singularity?
+## What is Apptainer?
 
-![](https://sylabs.io/guides/3.0/user-guide/_static/logo.png){height=250 fig-align=center}
+![](http://apptainer.org/static/hero-img-e614806cf573fd0cbbe09a25d9e69637.png){fig-align=center}
 
 ::: {.incremental}
 - Another software for working with containers, similar to Docker
@@ -183,6 +190,7 @@ docker run \
 ![](http://apptainer.org/static/hero-img-e614806cf573fd0cbbe09a25d9e69637.png){fig-align=center}
 
 ::: {.incremental}
+- Apptainer used to be 'Singularity'. 
 - In 2021 Singularity joined the Linux Foundation and became
   [Apptainer]{.green}.
 - The company [Sylabs]{.green} still maintains Singularity as a commercial

diff --git a/lectures/jupyter/jupyter.qmd b/lectures/jupyter/jupyter.qmd
@@ -42,63 +42,47 @@ _The next-generation interface for Jupyter_
 ![](https://jupyterlab.readthedocs.io/en/stable/_images/jupyterlab.png){height="100%" fig-align=center}
 ::::
 :::: {.column width="25%"}
-::: {.incremental}
+::: {.incremental .small}
 - Similar to an integrated development environments (IDE).
 - Tab views, Code consoles, Show output in a separate tab, Live rendering of edits _etc._
 - The jupyter lab interface can run Jupyter notebooks in the **main** work area
 :::
 ::::
 :::::
 
-## Using Jupyter notebooks {auto-animate="true" transition="none" transition-speed="fast" }
+## Using Jupyter notebooks
 
-::: {data-id="bullets"}
 - Document your work in markdown...
-:::
 
-::: {data-id="markdown1"}
 ``` {.default}
 **Penguin data analysis**
 
 Here we will investigate the [Penguin dataset](https://github.com/allisonhorst/palmerpenguins).
 
----
-
 The species included in this set are:
 
- - _Adelie_
- - _Chinstrap_
- - _Gentoo_
- ```
-:::
+- _Adelie_
+- _Chinstrap_
+- _Gentoo_
+```
 
-## Using Jupyter notebooks {auto-animate="true" transition="none" transition-speed="fast" }
+## Using Jupyter notebooks
 
-::: {data-id="bullets"}
 - Document your work in markdown...and have it rendered automatically.
-:::
-
-::: {data-id="markdown1"}
 
 **Penguin data analysis**
 
 Here we will investigate the [Penguin dataset](https://github.com/allisonhorst/palmerpenguins).
 
----
-
 The species included in this set are:
 
- - _Adelie_
- - _Chinstrap_
- - _Gentoo_
-:::
+- _Adelie_
+- _Chinstrap_
+- _Gentoo_
 
-## Using Jupyter notebooks {auto-animate="true" transition="none" transition-speed="fast" }
+## Using Jupyter notebooks
 
-::: {data-id="bullets"}
-- Document your work in markdown...and have it rendered automatically.
 - Execute code directly from the browser, with results attached to the code which generated them.
-:::
 
 ```{python}
 #| echo: true
@@ -108,51 +92,31 @@ data = sns.load_dataset("penguins")
 data.groupby("species").mean(numeric_only=True)
 ```
 
-## Using Jupyter notebooks {auto-animate="true" transition="none" transition-speed="fast" }
+## Using Jupyter notebooks
 
-::: {data-id="bullets"}
-- Document your work in markdown...and have it rendered automatically.
-- Execute code directly from the browser, with results attached to the code which generated them.
 - Mix and match languages in addition to `python`.
-:::
 
+::: {.fragment}
 **R**
 ```{python}
 #| echo: true
 %%R
 print(paste(Sys.Date(), ": Hello World", sep=""))
 ```
-
-## Using Jupyter notebooks {auto-animate="true" transition="none" transition-speed="fast" }
-
-::: {data-id="bullets"}
-- Document your work in markdown...and have it rendered automatically.
-- Execute code directly from the browser, with results attached to the code which generated them.
-- Mix and match languages in addition to `python`.
 :::
 
-**R**
-```{python}
-#| echo: true
-%%R
-print(paste(Sys.Date(), ": Hello World", sep=""))
-```
-
+::: {.fragment}
 **bash**
 ```{python}
 #| echo: true
 %%bash
 echo "$(date): Hello World!"
 ```
+:::
 
-## Using Jupyter notebooks {auto-animate="true" transition="none" transition-speed="fast" }
+## Using Jupyter notebooks
 
-::: {data-id="bullets"}
-- Document your work in markdown...and have it rendered automatically
-- Execute code directly from the browser, with results attached to the code which generated them
-- Mix and match languages in addition to `python`.
 - Generate plots directly in the browser and/or save to file.
-:::
 
 ```{python}
 #| echo: true