Renaming herbivores scripts

code/applications/herbivores/02_herbivores_clustering.R

@@ -3,10 +3,12 @@ library(dplyr)
 library(tidyr)
 library(here)
 
+application_name <- "herbivores"
+
 application_folder <- file.path(here(), "code", "applications", "herbivores")
 prepare_data_script_path <- file.path(
     application_folder,
-    "01_herbi_prepare_data.R"
+    sprintf("01_%s_prepare_data.R", application_name)
 )
 
 source(prepare_data_script_path)
@@ -35,8 +37,8 @@ stopifnot(
 message("Début du clustering des données Herbivores avec le modèle ", model)
 
 set.seed(1234, "L'Ecuyer-CMRG")
-base_data_folder <- file.path(here(), "code", "data", "herbivores")
-save_folder <- file.path(here(), "code", "results", "applications", "herbivores")
+base_data_folder <- file.path(here(), "code", "data", application_name)
+save_folder <- file.path(here(), "code", "results", "applications", application_name)
 
 if (!dir.exists(save_folder)) {
     dir.create(save_folder, recursive = TRUE)
@@ -59,7 +61,7 @@ list_collection <- clusterize_bipartite_networks(
 
 save_file <- file.path(
     save_folder, paste0(
-        "herbivore_collection_",
+        sprintf("%s_collection_", application_name),
         model, "_", start_time, ".Rds"
     )
 )

code/scripts/migale_application_herbivores.sh

@@ -0,0 +1,31 @@
+#!/usr/bin/env bash
+#$ -V
+#$ -cwd
+#$ -N herbivores_app
+#$ -m besa
+#$ -t 1:4
+#$ -q long.q
+#$ -pe thread 64
+#$ -M louis.lacoste+migale@agroparistech.fr
+#$ -o logs/$JOB_NAME.$TASK_ID
+#$ -e logs/$JOB_NAME.$TASK_ID
+
+# Creating log directory if it doesn't exists
+BASE_DIR="/home/$USER/work/mia-stage-2024"
+LOG_DIR=$(echo "$BASE_DIR/logs")
+
+if [ ! -d "$LOG_DIR" ]; then
+    mkdir -p $LOG_DIR
+fi
+
+# Constant data
+MODELARRAY=("iid" "pi" "rho" "pirho")
+
+MODEL=${MODELARRAY[$(($((SGE_TASK_ID - 1)) % 4))]}
+
+# Finding directory
+APPLICATIONS_DIR=$(echo "$BASE_DIR/code/applications")
+
+echo $APPLICATIONS_DIR
+
+Rscript "${APPLICATIONS_DIR}/herbivores/02_herbivores_clustering.R" --model $MODEL