Mercurial > repos > siwaa > redelac_stics_t

changeset 5:e0d592bb516e draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 1b434482800e773a592b5fc6f472e7df465e91ce"
author siwaa
date Fri, 22 Mar 2024 06:57:42 +0000
parents a41001337384
children b50500fdedf8
files redelacSticsTool.R redelacSticsTool.bash redelacSticsTool.xml
diffstat 3 files changed, 10 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/redelacSticsTool.R	Fri Feb 23 08:46:35 2024 +0000
+++ b/redelacSticsTool.R	Fri Mar 22 06:57:42 2024 +0000
@@ -236,10 +236,10 @@
     list_successive_usms <- list(vec)
 
     sim_options <- stics_wrapper_options(
-      javastics = javastics_path,
-      stics_exe = paste0(javastics_path, "/bin/stics_modulo"),
+      stics_exe = "stics_modulo",
       workspace = txt_path,
       verbose = TRUE,
+      force = TRUE,
       successive = list_successive_usms
     )
 
@@ -398,10 +398,9 @@
     mutate(P_usm = str_replace_all(P_usm, " ", "")) %>%
     mutate(wlieu = str_replace_all(wlieu, " ", "")) %>%
     mutate(stade = str_replace_all(stade, " ", "")) %>%
-    mutate(nomversion = str_replace_all(nomversion, " ", "")) %>%
-    mutate(across(3:9, as.numeric)) %>%
-    mutate(across(13:ncol(rap), as.numeric)) %>%
-    #separate(col=P_usm,into=c("upc","sol","systeme","rotation","tete_rotation","horizon","annee","culture"),sep="-",remove = FALSE)
+    mutate(nomversion = str_replace_all(P_usm, " ", "")) %>%
+    mutate(across(4:10, as.numeric)) %>%
+    mutate(across(14:ncol(rap), as.numeric)) %>%
     separate(
       col = USM,
       into = c(
--- a/redelacSticsTool.bash	Fri Feb 23 08:46:35 2024 +0000
+++ b/redelacSticsTool.bash	Fri Mar 22 06:57:42 2024 +0000
@@ -1,4 +1,7 @@
-cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0 . &&
+mkdir ./JavaSTICS-1.5.1-STICS-10.0.0 &&
+cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/logs JavaSTICS-1.5.1-STICS-10.0.0 &&
+cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/config JavaSTICS-1.5.1-STICS-10.0.0 &&
+cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/plant JavaSTICS-1.5.1-STICS-10.0.0 &&
 rm -rf JavaSTICS-1.5.1-STICS-10.0.0/config &&
 cp -r $4/config JavaSTICS-1.5.1-STICS-10.0.0 &&
 unzip -q $5 -d TMP &&
--- a/redelacSticsTool.xml	Fri Feb 23 08:46:35 2024 +0000
+++ b/redelacSticsTool.xml	Fri Mar 22 06:57:42 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="redelacSticsTool" name="redelacSticsTool" version="1.0.4">
+<tool id="redelacSticsTool" name="redelacSticsTool" version="1.0.6">
   <description>to run Stics for REDELAC</description>
   <requirements>
     <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:19459c8cfd37b747d704d59276791a27ae522b6b</container>