From c230aa02d60f4dede87aca342388981a4b9844d0 Mon Sep 17 00:00:00 2001
From: Insang Song <sigmafelix@hotmail.com>
Date: Tue, 12 Nov 2024 21:14:59 +0900
Subject: [PATCH] HMS calculation fix - upstream amadeus function was fixed -
 library argument is populated with dev library locations

---
 _targets.R              |  9 +++++----
 invalidate_container.sh | 25 +++++++++++++++++++++++++
 2 files changed, 30 insertions(+), 4 deletions(-)
 create mode 100755 invalidate_container.sh

diff --git a/_targets.R b/_targets.R
index eb067ca..9315f7c 100755
--- a/_targets.R
+++ b/_targets.R
@@ -2,6 +2,9 @@
 ##############################      BEETHOVEN      #############################
 ##### Main file controlling the settings, options, and sourcing of targets
 ##### for the beethoven analysis pipeline.
+.libPaths(
+  c("/mnt/lib-flex", .libPaths())
+)
 
 #############################      CONTROLLER      #############################
 default_controller <- crew::crew_controller_local(
@@ -20,10 +23,6 @@ targets::tar_config_set(store = "/opt/_targets")
 
 ##############################       OPTIONS      ##############################
 
-.libPaths(
-  c("/mnt/lib-flex", .libPaths())
-)
-
 
 targets::tar_option_set(
   packages = c(
@@ -31,6 +30,8 @@ targets::tar_option_set(
     "data.table", "sf", "crew", "crew.cluster",
     "amadeus"
   ),
+  # add
+  library = c("/mnt/lib-flex", .libPaths()),
   repository = "local",
   error = "continue",
   memory = "transient",
diff --git a/invalidate_container.sh b/invalidate_container.sh
new file mode 100755
index 0000000..0c63854
--- /dev/null
+++ b/invalidate_container.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+DEBUG_TARGET=$1
+
+#SBATCH --job-name=beethoven
+#SBATCH --mail-user=manwareme@nih.gov
+#SBATCH --mail-type=END,FAIL
+#SBATCH --partition=geo
+#SBATCH --ntasks=1
+#SBATCH --mem=100G
+#SBATCH --cpus-per-task=50
+#SBATCH --error=/ddn/gs1/home/manwareme/beethoven/beethoven/slurm/beethoven_%j.err
+#SBATCH --output=/ddn/gs1/home/manwareme/beethoven/beethoven/slurm/beethoven_%j.out
+
+# run pipeline in the container
+apptainer exec \
+  --bind $PWD:/mnt \
+  --bind $PWD/inst:/inst \
+  --bind /ddn:/input \
+  --bind $PWD/_targets:/opt/_targets \
+  beethoven_dl_calc.sif \
+  Rscript --no-init-file -e "targets::tar_invalidate('$DEBUG_TARGET')"
+
+# run interactive R session in the container
+# apptainer exec --bind $PWD/inst:/inst --bind /ddn/gs1/group/set/Projects/NRT-AP-Model/input:/input --bind $PWD:/mnt beethoven_dl_calc.sif R
\ No newline at end of file