Merge pull request #273 from NBISweden/snakemake-lecture

Snakemake lecture

assets/css/styles.scss

@@ -116,6 +116,10 @@ $footer-fg: DimGray;
 
 /* code */
 
+pre, code, .sourceCode {
+  font-size: 0.75rem;
+}
+
 pre {
   line-height: 1.4;
   background-color: $code-block-bg;

home_precourse.qmd

@@ -284,38 +284,48 @@ into some problems with certain Conda packages that have not yet been built for
 the ARM64 architecture. The [Rosetta](https://support.apple.com/en-us/HT211861)
 software allows ARM64 Macs to use software built for the old AMD64 architecture,
 which means you can always fall back on creating AMD/Intel-based environments
-and use them in conjunction with Rosetta. This is how you do it:
+and use them in conjunction with Rosetta. This can be done by specifying
+`--subdir osx-64` when creating the environment, _e.g._:
+
+```bash
+conda env create -f <path-To-Environment.yml> --subdir osx-64
+```
+
+or
+
+```bash
+conda create -n myenv <packages...> --subdir osx-64
+```
+
+::: {.callout-important}
+To make sure that subsequent installations into this environment also use the
+`osx-64` architecture, activate the environment and then run:
 
 ```bash
-CONDA_SUBDIR=osx-64 <conda-command>
-conda activate <env>
 conda config --env --set subdir osx-64
 ```
+:::
 
-The first command creates the Intel-based environment, while the last one
-makes sure that subsequent commands are also using the Intel architecture. If
-you don't want to remember and do this manually each time you want to use
-AMD64/Rosetta you can check out [this bash script](https://github.com/fasterius/dotfiles/blob/main/scripts/intel-conda-env.sh).
 
 ## Installing Snakemake
 
 We will use Conda environments for the set up of this tutorial, but don't worry
 if you don't understand exactly what everything does - you'll learn all the
 details at the course. First make sure you're currently situated inside the
 tutorials directory (`workshop-reproducible-research/tutorials`) and then create
-the Conda environment like so:
+and activate the Conda environment with the commands below:
+
+::: {.callout-caution title="ARM64 users"}
+Some of the packages in this environment are not available for the ARM64
+architecture, so you'll have to add `--subdir osx-64` to the `conda env create`
+command. See the [instructions above](#conda-on-new-macs) for more details.
+:::
 
 ```bash
 conda env create -f snakemake/environment.yml -n snakemake-env
 conda activate snakemake-env
 ```
 
-::: {.callout-caution title="ARM64 users"}
-Some of the packages in this environment is not available for the ARM64
-architecture, so you'll have to follow the [instructions
-above](#conda-on-new-macs).
-:::
-
 Check that Snakemake is installed correctly, for example by executing `snakemake
 --help`. This should output a list of available Snakemake settings. If you get
 `bash: snakemake: command not found` then you need to go back and ensure that