Merge pull request #71 from NBISweden/dev-percyfal

Dev percyfal

.pre-commit-config.yaml

@@ -86,6 +86,7 @@ repos:
           docs/slides/datageneration/index\.qmd|
           docs/slides/foundations/index\.qmd|
           docs/slides/variant_filtering/index\.qmd|
+          docs/slides/variant_calling/index\.qmd|
           docs/exercises/variant_filtering/index\.qmd|
           docs/slides/simulation/index\.qmd
           )$

docs/_data.yml

@@ -82,6 +82,7 @@ __yellow_recal_bam__:
 
 __reference__:
   - M_aurantiacus_v1.fasta: monkeyflower/tiny/M_aurantiacus_v1_splitline_ordered.fasta
+  - M_aurantiacus_v1.fasta.fai: monkeyflower/tiny/M_aurantiacus_v1_splitline_ordered.fasta.fai
 
 __sampleinfo__:
   - monkeyflower/sampleinfo.csv
@@ -137,3 +138,22 @@ exercises/genetic_diversity:
 
 slides/foundations:
   - data/Homo_sapiens: Homo_sapiens
+
+slides/variant_calling:
+  - monkeyflower/tiny/PUN-R-ELF/PUN-R-ELF_R1.fastq.gz
+  - monkeyflower/tiny/PUN-R-ELF/PUN-R-ELF_R2.fastq.gz
+  - monkeyflower/tiny/PUN-R-ELF/PUN-R-ELF.sort.dup.bam
+  - monkeyflower/tiny/PUN-R-ELF/PUN-R-ELF.sort.dup.bai
+  - monkeyflower/tiny/PUN-R-ELF/PUN-R-ELF.sort.dup.recal.bam
+  - monkeyflower/tiny/PUN-R-ELF/PUN-R-ELF.sort.dup.recal.bai
+  - monkeyflower/tiny/PUN-Y-INJ/PUN-Y-INJ_R1.fastq.gz
+  - monkeyflower/tiny/PUN-Y-INJ/PUN-Y-INJ_R2.fastq.gz
+  - monkeyflower/tiny/PUN-Y-INJ/PUN-Y-INJ.sort.dup.recal.bam
+  - monkeyflower/tiny/PUN-Y-INJ/PUN-Y-INJ.sort.dup.recal.bai
+  - monkeyflower/tiny/PUN-Y-INJ/PUN-Y-INJ.sort.dup.bam
+  - monkeyflower/tiny/PUN-Y-INJ/PUN-Y-INJ.sort.dup.bai
+  - monkeyflower/small/redyellow.variantsites.vcf.gz
+  - monkeyflower/small/redyellow.variantsites.vcf.gz.tbi
+  - allsites.vcf.gz: monkeyflower/tiny/redyellow.allsites.vcf.gz
+  - allsites.vcf.gz.tbi: monkeyflower/tiny/redyellow.allsites.vcf.gz.tbi
+  - __reference__

docs/_quarto.yml

@@ -17,20 +17,27 @@ project:
     - "syllabus.qmd"
     # Exercises
     # - "exercises/data.qmd"
+    - "exercises/index.qmd"
     - "exercises/compute_environment/index.qmd"
     - "exercises/datasets/monkeyflowers.qmd"
-    - "exercises/index.qmd"
     - "exercises/simulation/index.qmd"
     - "exercises/variant_calling/index.qmd"
     - "exercises/variant_filtering/index.qmd"
+    - "exercises/genetic_diversity/index.qmd"
+    - "exercises/population_structure/index.qmd"
+    - "exercises/demography/index.qmd"
+    - "exercises/selection/index.qmd"
     # Slides
     - "slides/index.qmd"
     - "slides/pgip/index.qmd"
     - "slides/foundations/index.qmd"
     - "slides/simulation/index.qmd"
-    # - "slides/variant_calling/index.qmd"
-    # - "slides/datageneration/index.qmd"
+    - "slides/variant_calling/index.qmd"
+    - "slides/variant_filtering/index.qmd"
+    - "slides/genetic_diversity/index.qmd"
     - "slides/population_structure/index.qmd"
+    - "slides/demography/index.qmd"
+    - "slides/selection/index.qmd"
     # Recipes
     - "recipes/index.qmd"
     - "recipes/slim/index.qmd"
@@ -62,6 +69,7 @@ format:
     quarto-required: ">=1.2.475"
     toc: true
     include-after-body: assets/www/logo-hyperlink.html
+    include-before: [ '<script type="text/x-mathjax-config">MathJax.Hub.Config({tex2jax: {enableAssistiveMml: false}});</script>']
     toc-depth: 1
     slide-level: 2
     slide-number: true
@@ -73,9 +81,14 @@ format:
     fig-align: left
     fig-height: 12
     fig-width: 10
+    # All three combinations have same aspect ratio
     width: 1280
     height: 720
-    margin: 0.1
+    # width: 1920
+    # height: 1080
+    # width: 1600
+    # height: 900
+    margin: 0.08
     date: last-modified
     date-format: "DD-MMM-YYYY"
     navigation-mode: vertical
@@ -97,13 +110,13 @@ revealjs-plugins:
   - pointer
 
 execute:
-  cache: true
+  cache: false
   echo: true
   warning: false
   include: true
   autodep: true
   eval: true
-  error: true
+  error: false
 
 knitr:
   opts_chunk:

docs/assets/css/custom.scss

@@ -162,7 +162,6 @@ code.large {
 
 .flushright {
   float: right;
-  font-size: 70%;
 }
 
 .translatey50 {

docs/exercises/compute_environment/index.qmd

@@ -13,7 +13,7 @@ format: html
 
 <!-- markdownlint-enable MD041 -->
 
-## UPPMAX
+## {{< fa server >}} UPPMAX
 
 ::: {.callout-important collapse=true}
 
@@ -74,23 +74,29 @@ UPPMAX hosts tutorials and user guides at
 <https://www.uppmax.uu.se/support/user-guides/guide--first-login-to-uppmax/>
 has information on how to connect to and work on UPPMAX.
 
-## JupyterLite
+## {{< fa laptop >}} Jupyter Notebooks
 
-Some exercises will be run using
-[JupyterLite](https://github.com/jupyterlite/jupyterlite) which is a
-JupyterLab distribution that runs entirely in the browser. Apart from
-having a browser, no preparations are necessary. Note that some users
-have reported issues with Firefox and that Google Chrome may be a
-better solution.
+[Jupyter Notebook](https://jupyter.org/) exercises will be run in
+local compute environments on your laptop. See the section below on
+setting up a `pgip` conda environment, which by default installs `jupyter` and its dependencies.
 
-## Fallback solution: conda
+### {{< fa brands firefox >}} JupyterLite
 
-In case there are issues with the HPC, a fallback option is to install
-software packages locally on your computer. We will use the
-[conda](https://docs.conda.io/en/latest/) package manager to install
-necessary requirements from the package repositories
+There are some Jupyter Notebook exercises that are hosted online and
+run using [JupyterLite](https://github.com/jupyterlite/jupyterlite)
+which is a JupyterLab distribution that runs entirely in the browser.
+Apart from having a browser, no preparations are necessary. Note that
+some users have reported issues with Firefox and that Google Chrome
+may be a better solution.
+
+## {{< fa laptop >}} Conda {#sec-compute-environment-conda}
+
+Exercises that require local software installation will make use of
+the [conda](https://docs.conda.io/en/latest/) package manager to
+install necessary requirements from the package repositories
 [bioconda](https://bioconda.github.io/) and
-[conda-forge](https://conda-forge.org/).
+[conda-forge](https://conda-forge.org/). This is also the fallback
+solution in case there are issues with the HPC.
 
 ### 1. Install conda
 
@@ -124,28 +130,38 @@ Please note that the order of these commands is important!
 ### 3. Create an isolated course environment
 
 It is suggested you create and change to a isolated environment `pgip`
-dedicated to the course. We also suggest you use
-[mamba](https://mamba.readthedocs.io/en/latest/index.html) package
-manager to install programs as this is much quicker.
+dedicated to the course. The command below will create an environment
+named `pgip` and install the packages `python` version 3.10, an R base
+installation (`r-base`), the `jupyter` package that provides support
+for Jupyter Notebooks, and the `mamba` package manager.
 
 ```{bash }
 #| label: create-conda-pgip
 #| echo: true
 #| eval: false
-mamba create -n pgip python=3.10 r-base
-mamba activate pgip
+conda create --name pgip python=3.10 r-base jupyter mamba
+conda activate pgip
 ```
 
-To deactivate an environment you issue the command `mamba deactivate`.
+The `activate` command is required to access the isolated environment
+named `pgip`. Once you have activated the environment, you gain access
+to whatever programs are installed. To deactivate an environment you
+issue the command `conda deactivate`.
 
 ### 4. Install packages
 
-You can install packages as follows (remember to activate `pgip`!):
+Installation of packages in an environment is done with the `install`
+command, but we recommend you use the
+[mamba](https://mamba.readthedocs.io/en/latest/index.html) package
+manager as it is faster (`mamba` is a rewrite of `conda` in C++). An
+example of how to install packages `bcftools, angsd, mosdepth` follows
+(remember to activate `pgip`!):
 
 ```{bash }
 #| label: conda-install-packages
 #| echo: true
 #| eval: false
+conda activate pgip
 mamba install bcftools angsd mosdepth
 ```
 
@@ -191,13 +207,10 @@ Example:
 #| label: uppmax-load-modules
 #| echo: true
 #| eval: false
-module load uppmax bioinfo-tools bwa/0.7.17 FastQC/0.11.9
+module load uppmax bioinfo-tools bwa/0.7.17 \
+    FastQC/0.11.9
 ```
 
-:::
-
-:::
-
 #### Conda
 
 Provides a [conda environment
@@ -218,4 +231,8 @@ dependencies:
   - fastqc=0.12.1
 ```
 
+:::
+
+:::
+
 ## References

docs/exercises/demography/index.qmd

@@ -0,0 +1,77 @@
+---
+title: "Demographic inference"
+author:
+  - "André Soares"
+  - "Per Unneberg"
+format: html
+---
+
+::: {.callout-important collapse=true}
+
+#### {{< fa server >}} Compute environment setup
+
+If you haven't already done so, please read [Compute
+environment](../compute_environment/index.qmd) for information on how
+to prepare your working directory.
+
+:::
+
+::: {.callout-tip collapse=true}
+
+## Learning objectives
+
+:::
+
+::: {.callout-note collapse=true}
+
+## Data setup
+
+:::{.panel-tabset}
+
+#### UPPMAX
+
+#### Local
+
+:::
+
+:::
+
+::: {.callout-note collapse=true}
+
+## Tools
+
+:::{.panel-tabset}
+
+#### Listing
+
+- [psmc](https://github.com/lh3/psmc) [@li_InferenceHumanPopulation_2011]
+
+#### UPPMAX modules
+
+Execute the following command to load modules:
+
+```{bash }
+#| label: uppmax-load-modules
+#| echo: true
+#| eval: false
+module load uppmax bioinfo-tools \
+    psmc/0.6.5-r67-e5f7df5
+```
+
+#### Conda
+
+Copy the contents to a file `environment.yml` and install packages
+with `mamba env update -f environment.yml`.
+
+```{lang="text" }
+channels:
+  - conda-forge
+  - bioconda
+  - default
+dependencies:
+  - psmc
+```
+
+:::
+
+:::