Update MGnifyR repo (#42)

Taskfile.yml

@@ -1,5 +1,8 @@
 version: '3'
 
+env:
+  NB_DOCKER_EXE: "docker"
+
 tasks:
   add-py-notebook:
     summary: |
@@ -43,7 +46,7 @@ tasks:
 
       The files in src/notebooks are mounted as editable, and served on port 8888.
     cmds:
-      - docker run -it -v $PWD/src/notebooks:/home/jovyan/mgnify-examples -p 8888:8888 quay.io/microbiome-informatics/emg-notebooks.dev:latest
+      - $NB_DOCKER_EXE run -it -v $PWD/src/notebooks:/home/jovyan/mgnify-examples -p 8888:8888 quay.io/microbiome-informatics/emg-notebooks.dev:latest
 
   build-notebook-docker:
     summary: |
@@ -53,15 +56,15 @@ tasks:
 
       NOT needed if you're just editing/adding notebooks with no additional dependencies.
     cmds:
-      - docker build --load -f docker/Dockerfile -t quay.io/microbiome-informatics/emg-notebooks.dev:latest .
+      - $NB_DOCKER_EXE build --load -f docker/Dockerfile -t quay.io/microbiome-informatics/emg-notebooks.dev:latest .
 
   build-static-docker:
     summary: |
       Builds a docker image with Quarto included, for statically rendering the notebook outputs.
 
       The built image is tagged as `notebooks-static`.
     cmds:
-      - docker build --load -f docker/docs.Dockerfile -t notebooks-static .
+      - $NB_DOCKER_EXE build --load -f docker/docs.Dockerfile -t notebooks-static .
     sources:
       - docker/docs.Dockerfile
       - docker/Dockerfile
@@ -72,7 +75,7 @@ tasks:
 
       The site is built to ./_site
     cmds:
-      - docker run -it -v $PWD:/opt/repo -w /opt/repo notebooks-static render --execute
+      - $NB_DOCKER_EXE run -it -v $PWD:/opt/repo -w /opt/repo notebooks-static render --execute
     deps: [build-static-docker]
     sources:
       - src/**/*
@@ -84,15 +87,15 @@ tasks:
       This serves the contents of ./_site
     cmds:
       - echo "Browse to http://127.0.0.1:4444"
-      - docker run -it -v $PWD:/opt/repo -w /opt/repo/_site -p 4444:4444 --entrypoint python notebooks-static -m http.server 4444
+      - $NB_DOCKER_EXE run -it -v $PWD:/opt/repo -w /opt/repo/_site -p 4444:4444 --entrypoint python notebooks-static -m http.server 4444
     deps: [render-static]
 
   preview-static:
     summary: |
       Runs, renders, and serves the notebooks as a static website, watching for changes
     cmds:
       - echo 'When the rendering is finished, the static preview of notebooks will be at http://127.0.0.1:4444 ...'
-      - docker run -it -v $PWD:/opt/repo -w /opt/repo -p 4444:4444 notebooks-static preview --no-browser --port 4444 --host 0.0.0.0
+      - $NB_DOCKER_EXE run -it -v $PWD:/opt/repo -w /opt/repo -p 4444:4444 notebooks-static preview --no-browser --port 4444 --host 0.0.0.0
     deps: [build-static-docker]
 
   update-mgnifyr-cache:
@@ -105,4 +108,4 @@ tasks:
 
       It writes a zip of the cache to dependencies/mgnify-cache.tgz
     cmds:
-      - docker run -it -v $PWD/dependencies:/opt/dependencies -w /opt/dependencies quay.io/microbiome-informatics/emg-notebooks.dev:latest /bin/bash zip-mgnifyr-cache.sh
+      - $NB_DOCKER_EXE run -it -v $PWD/dependencies:/opt/dependencies -w /opt/dependencies quay.io/microbiome-informatics/emg-notebooks.dev:latest /bin/bash zip-mgnifyr-cache.sh

dependencies/dependencies.R

@@ -3,4 +3,4 @@
 # Extra pacakges not installed in Docker image, or installable via Conda:
 
 require("devtools")
-devtools::install_github("beadyallen/MGnifyR")
+devtools::install_github("EBI-Metagenomics/MGnifyR", ref="d1baca93465f8c97101049bd66b63a8bb5a0d6ab")