Update installation instructions and package list

Makefile

@@ -40,16 +40,16 @@ install-pgip: ## Create pgip environment and install packages to render site
 	if conda env list | cut -f1 -d ' ' | grep -q "${PGIP}$$"; then \
 		echo "Environment exists; skipping install"; \
 	else \
-		mamba env create -n ${PGIP} --file environment.yml; \
+		mamba env create -n ${PGIP} conda-linux-64.lock; \
 	fi;
 
 install-dev: install-pgip ## Install additional development tools
 	mamba env update -n ${PGIP} --file environment-dev.yml
 
 install-R: install-pgip ## Install additional R packages that require manual installation
 	R -e "install.packages('dotenv', repos=c(CRAN = 'https://cran.rstudio.com/'))"
-	R -e "tinytex::tlmgr_update()"
-	R -e "tinytex::reinstall_tinytex(force=TRUE)"
+	#R -e "tinytex::tlmgr_update()"
+	#R -e "tinytex::reinstall_tinytex(force=TRUE)"
 	R -e "library(devtools); devtools::install_local('src/R/pgip')"
 
 install-kernels: install-pgip ## Install python and bash kernel

README.md

@@ -58,7 +58,6 @@ environment variable:
     conda activate pgip
     make install-R
     make install-kernels
-    make install-bcftools
     make install-pixy
     make install-dev
 
@@ -73,9 +72,9 @@ issues](#installation-issues).
 
 ### Create pgip conda environment
 
-Create a conda environment called `pgip` using the environment file
+Create a conda environment called `pgip` using the conda lock file
 
-    mamba env create --file environment.yml
+    mamba env create -n pgip conda-linux-64.lock
 
 and activate the environment
 
@@ -123,7 +122,10 @@ information.
 
 [Install Quarto](https://quarto.org/docs/get-started) version [Quarto\>=1.2.475](https://quarto.org/docs/download/).
 
-### bcftools manual install
+### bcftools manual install (OBSOLETE)
+
+**OBSOLETE**: installing pgip using `conda-linux-64.lock` obviates the
+need to install bcftools manually.
 
 Due to dependency issues, bcftools has to be manually installed:
 

docs/exercises/variant_filtering/index.qmd

@@ -29,7 +29,7 @@ In this exercise we will look at ways of filtering variant data. We
 will begin by applying filters to the variant file containing all
 sites data, followed by a more general approach based on sequencing
 coverage that works also when the variant file lacks information about
-monomorphic sites.
+invariant sites.
 
 ::: {.callout-tip collapse=true}
 
@@ -348,7 +348,6 @@ csvtk summary -t -f MEAN_DEPTH:mean ${OUT}.idepth
 data <- read.table("vcftools/allsites.idepth", header=TRUE)
 LDEPTH_MEAN <- round(mean(data$MEAN_DEPTH), 1)
 ldepth <- sprintf("%.1fX", LDEPTH_MEAN)
-
 ```
 
 Note that `vcftools` treats uncalled sites as missing data, which is
@@ -374,7 +373,10 @@ total depth across all samples.
 
 We plot the distribution of depths by counting how many times each
 depth is observed. This can be done with `csvtk summary` where we
-count positions and group (`-g`) by the `SUM_DEPTH` value:
+count positions and group (`-g`) by the `SUM_DEPTH` value:^[Viewing
+`csvtk` output: either you can **redirect** (`>`) the results from
+`csvtk` to a png output file, or you can **pipe** (`|`) it to the
+command `display`, which should fire up a window with your plot.]
 
 ```{bash }
 #| label: csvtk-plot-vcftools-depth-per-site

docs/slides/foundations/index.qmd

@@ -18,7 +18,7 @@ format:
 #| echo: false
 #| eval: true
 #| cache: false
-library(viridislite)
+library(viridisLite)
 library(gganimate)
 library(patchwork)
 library(expm)
@@ -444,6 +444,10 @@ The latter expression is called the *nucleotide diversity*
 
 ## Alleles as algebraic entities
 
+:::: {.columns}
+
+::: {.column width="50%"}
+
 Recall: **alleles** refer to *different variants* of a sequence at a
 locus (genomic position).
 
@@ -467,32 +471,31 @@ Will use combination $A$, $a$ for *bi-allelic* loci from now on
 
 :::
 
-::: {.fragment .large}
+:::
+
+::: {.column width="50%"}
+
+::: {.fragment}
 
 ::: {.callout-important appearance="simple" icon=false}
 
 ### Example: gene coding for flower color
 
 :::::: {.columns}
 
-::::: {.column width="30%"}
+::::: {.column width="50%"}
 
 [{{< fa solid circle >}}]{style="color: #ff2a2a;"} $A$ red color
 
 {{< fa regular circle >}} $a$ white color
 
-:::::
-
-:::::{.column width="5%"}
-
-:::::
-
-:::::{.column width="20%" .fragment}
+::: {.fragment}
 
 [Punnett square](https://en.wikipedia.org/wiki/Punnett_square)
 
 :::: {style="display: grid; grid-template-columns: auto auto auto;
-grid-row-gap: 0px; grid-column-gap: 0px; text-align: center; align-items: center;"}
+grid-row-gap: 0px; grid-column-gap: 0px; text-align: center;
+align-items: center;"}
 
 :::{}
 
@@ -520,13 +523,13 @@ A
 
 :::{}
 
-![](assets/images/flower-red.svg){width=100}
+![](assets/images/flower-red.svg){width=75}
 
 :::
 
 :::{}
 
-![](assets/images/flower-pink.svg){width=100}
+![](assets/images/flower-pink.svg){width=75}
 
 :::
 
@@ -538,25 +541,27 @@ a
 
 :::{}
 
-![](assets/images/flower-pink.svg){width=100}
+![](assets/images/flower-pink.svg){width=75}
 
 :::
 
 :::{}
 
-![](assets/images/flower-white.svg){width=100}
+![](assets/images/flower-white.svg){width=75}
 
 :::
 
 ::::
 
+:::
+
 :::::
 
 :::::{.column width="5%"}
 
 :::::
 
-::::: {.column width="40%" .fragment}
+::::: {.column width="45%" .fragment}
 
 :::: {style="display: grid; grid-template-columns: 1fr 1fr 1fr 1fr;
 grid-row-gap: 0px; grid-column-gap: 10px; text-align: center; align-items: center;"}
@@ -621,6 +626,10 @@ Heterozygote has intermediate color phenotype (pink).
 
 :::
 
+:::
+
+::::
+
 ::: {.notes}
 
 Until now the examples have been based on nucleotide sequences.
@@ -4218,6 +4227,7 @@ xi <- L / 2
 #| fig-align: center
 #| fig-height: 5
 #| fig-width: 10
+#| fig-format: png
 #| fig-cap: The effect of a selective sweep on
 #|     diversity. The arrow points to the site under selection.
 #|     The y-axis shows Tajima's D which is proportional to the

environment-dev.yml

@@ -1,16 +1,14 @@
+# Development environment
 name: pgip-dev
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
   - conda-lock
-  - pip
   - pre-commit
   - r-docopt
-  - r-fontawesome
   - r-languageserver
-  - r-leaflet
   - r-lintr
   - r-precommit
   - pip:

environment.yml

@@ -9,6 +9,7 @@ dependencies:
   - bedtools
   - bcftools
   - bokeh
+  - bwa
   - ca-certificates
   - csvtk
   - cyvcf2=0.30.16
@@ -25,10 +26,11 @@ dependencies:
   - multiqc
   - pandas
   - pip
+  - picard
   - pyslim
   - python>=3.10
   - python-newick
-  # - r-animation
+  - qualimap
   - r-ape
   - r-codetools
   - r-curl
@@ -48,8 +50,6 @@ dependencies:
   - r-gsalib
   - r-highcharter
   - r-igraph
-  # # - r-irkernel
-  # # - r-jsonlite
   - r-kableextra
   - r-latex2exp
   - r-leaflet
@@ -58,20 +58,16 @@ dependencies:
   - r-patchwork
   - r-pdftools
   - r-plotly
-  # # - r-reactable
   - r-readr
   - r-readxl
   - r-reticulate
   - r-rmarkdown>=2.19
   - r-tidyr
-  # # - r-transformr
   - r-viridis
   - samtools=1.15.1
-  # # - scikit-learn
   - scikit-allel
   - slim>=4.0
   - sgkit
   - tskit>=0.5.0
+  - vcflib
   - vcftools
-  # # - tqdm
-  # # - yarl

scripts/condalock.sh

@@ -4,7 +4,7 @@ set -xeuo pipefail
 if [[ $# == 1 ]]; then
     if [[ "$1" == "--force" ]]; then
         echo "generating conda-linux-64.lock from environment.yml"
-        conda-lock --kind explicit --platform linux-64
+        conda-lock lock -f environment.yml --kind explicit --platform linux-64
     else
         echo "Usage: $0 [--force]"
         exit 1