Merge pull request #368 from NIEHS/container-01

set up container, def, and archive old bash scripts
NIEHS · Oct 1, 2024 · 45a2170 · 45a2170
2 parents 524fcd7 + bad244e
commit 45a2170
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diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
 
 name: R-CMD-check
 

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
 
 name: lint
 

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
   release:
     types: [published]
   workflow_dispatch:

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -3,9 +3,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
 
 name: test-coverage-local
 

diff --git a/init_targets_storage.sh → archive/init_targets_storage.sh b/init_targets_storage.sh → archive/init_targets_storage.sh
diff --git a/run_interactive.sh → archive/run_interactive.sh b/run_interactive.sh → archive/run_interactive.sh
diff --git a/run_slurm.sh → archive/run_slurm.sh b/run_slurm.sh → archive/run_slurm.sh
diff --git a/setup_hook.sh → archive/setup_hook.sh b/setup_hook.sh → archive/setup_hook.sh
diff --git a/container/beethoven_dl_calc.def b/container/beethoven_dl_calc.def
@@ -0,0 +1,46 @@
+BootStrap: docker
+From: rocker/geospatial:latest
+
+%files
+    /ddn/gs1/tools/set/R432/lib64/R/library /R_packages
+
+
+%post
+    # Update package list
+    apt-get update
+
+    # Install locales and generate the necessary locale
+    apt-get install -y locales
+    locale-gen en_US.UTF-8
+
+    # Install fonts for Unicode support
+    apt-get install -y fonts-dejavu fonts-liberation fonts-noto fonts-unifont
+
+    # Set locale for the environment
+    echo "LANG=en_US.UTF-8" >> /etc/default/locale
+    echo "LC_ALL=en_US.UTF-8" >> /etc/default/locale
+    export LANG=en_US.UTF-8
+    export LC_ALL=en_US.UTF-8
+
+
+    mkdir /pipeline
+    mkdir /input
+    mkdir /opt/_targets
+
+    Rscript -e "install.packages(c('pak','targets','tarchetypes','crew','crew.cluster'))"
+    Rscript -e "pak::pkg_install('NIEHS/amadeus')"
+    Rscript -e "remotes::install_github('NIEHS/beethoven')"
+
+
+
+
+%environment
+    # Set locale for the container environment
+    export LANG=en_US.UTF-8
+    export LC_ALL=en_US.UTF-8
+    export TERM=xterm-256color
+
+%runscript
+
+%labels
+  basic geospatial with targets and crew plus unicode text so the target progress prints nicely