Test tags and see if this builds a dev package with github version of…

… dada2

.github/workflows/docker-ci.yml

@@ -9,6 +9,8 @@ on:
   push:
     branches:
       - dev
+    tags:
+      - 'v*'
   release:
     types: [published]
 
@@ -47,6 +49,11 @@ jobs:
         uses: docker/metadata-action@v5
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
 
       # Build and push Docker image with Buildx (don't push on PR)
       # https://github.com/docker/build-push-action

dockerfiles/R/Dockerfile

@@ -1,4 +1,4 @@
-FROM rocker/verse:4.3.2
+FROM rocker/verse:4.4.2
 #Modified from here https://github.com/davismcc/r-tidybioc-img/blob/master/Dockerfile
 LABEL description="Docker image containing DADA2, DECIPHER, phangorn, and latest R with tidyverse and Bioconductor packages"
 

dockerfiles/R/install.R

@@ -4,19 +4,23 @@ install.packages("BiocManager")
 BiocManager::install()
 
 pkgs <- c(
+  "devtools",
   "RCurl",
   "tidyverse",
   "pander",
   "phangorn",
   "dplyr",
-  "dada2",
+  # "dada2",
   "DECIPHER",
   "digest",
   "biomformat",
   "optparse",
   "yaml"
 )
 
+# developer (Github) URLs; dev branch only for now
+dev <- c("benjjneb/dada2")
+
 # check that desired packages are available
 ap.db <- available.packages(contrib.url(BiocManager::repositories()))
 ap <- rownames(ap.db)
@@ -29,6 +33,8 @@ pkgs_to_install <- pkgs_to_install[!(pkgs_to_install %in% ip)]
 
 BiocManager::install(pkgs_to_install)
 
+if (length(dev) > 0) { lapply(dev, devtools::install_github, upgrade = "never") }
+
 ## just in case there were warnings, we want to see them
 ## without having to scroll up:
 warnings()