Mercurial > repos > siwaa > redelac_stics_s

changeset 10:65c00476f417 draft default tip

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"planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4a2264991516b494ed11d1a7d5260ba543696a04/tools/REDELACSticsSimulator commit 4a2264991516b494ed11d1a7d5260ba543696a04-dirty"
author siwaa
date Fri, 27 Oct 2023 09:15:25 +0000
parents 52877f7c9d6b
children
files redelacSticsSimulator.R redelacSticsSimulator.bash redelacSticsSimulator.xml
diffstat 3 files changed, 26 insertions(+), 20 deletions(-) [+]
line wrap: on
line diff
--- a/redelacSticsSimulator.R	Tue Oct 17 11:21:34 2023 +0000
+++ b/redelacSticsSimulator.R	Fri Oct 27 09:15:25 2023 +0000
@@ -9,6 +9,7 @@
 library(dplyr)
 library(stringr)
 library(readr)
+library(doFuture)
 
 sessionInfo()
 
@@ -50,11 +51,9 @@
 rotation <- successRef$rotation[1]
 
 if (parallel) {
-  cl <- makeCluster(nbSlots)
-  print("Inside R, info on the cluster:")
-  print(cl)
-  registerDoParallel(cl)
-  `%dordopar%` <- `%dopar%`
+  doFuture::registerDoFuture()
+  future::plan(multisession, workers = nbSlots)
+  `%dordopar%` <- `%dofuture%`
 } else {
   `%dordopar%` <- `%do%`
 }
@@ -75,10 +74,9 @@
 result <- foreach(j = 1:length(casesUpcSol)) %:%
   foreach(
     i = 1:nrow(successive_usms_tab_split[[j]]),
-    .packages = c("foreach", "SticsRFiles", "SticsOnR")
+    .options.future = list(packages =c("foreach", "SticsRFiles", "SticsOnR"))
+
   ) %dordopar% {
-    if (parallel)
-      sink("./logPaRedelac.txt", append = TRUE)
 
     nusms <- as.numeric(successive_usms_tab_split[[j]][i, 2])
 
@@ -97,18 +95,12 @@
 
     list_usms <- vec
 
-    cat(paste0("-->", successive_usms_tab_split[[j]][i, 1], "launched\n"))
+    cat(paste0("--> succession : ", successive_usms_tab_split[[j]][i, 1], " launched\n"))
 
     return(stics_wrapper(model_options = sim_options, situation = list_usms))
 
   }
 
-if (parallel) {
-  stopCluster(cl)
-  sink()
-  cat(read_file("./logPaRedelac.txt"))
-}
-
 for (j in  1:length(casesUpcSol)) {
   splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
 
--- a/redelacSticsSimulator.bash	Tue Oct 17 11:21:34 2023 +0000
+++ b/redelacSticsSimulator.bash	Fri Oct 27 09:15:25 2023 +0000
@@ -14,7 +14,7 @@
 cat ./bashlog &&
 echo "=================================" && 
 cd WS &&
-/usr/bin/time -p -o ./bashlog zip -qq -r analyse_simulations_STICS analyse_simulations_STICS &&
+/usr/bin/time -p -o ./bashlog zip $9 -qq -r analyse_simulations_STICS analyse_simulations_STICS &&
 echo "Step 2, time to zip the results:" &&
 echo "================================" && 
 cat ./bashlog &&
@@ -23,7 +23,7 @@
 rm -rf analyse_simulations_STICS &&
 cd .. &&
 mv WS $WSname &&
-/usr/bin/time -p -o ./bashlog zip -qq -r $WSname $WSname &&
+/usr/bin/time -p -o ./bashlog zip $9 -qq -r $WSname $WSname &&
 echo "Step 3, time to zip the Workspace:" &&
 echo "==================================" && 
 cat ./bashlog &&
--- a/redelacSticsSimulator.xml	Tue Oct 17 11:21:34 2023 +0000
+++ b/redelacSticsSimulator.xml	Fri Oct 27 09:15:25 2023 +0000
@@ -1,11 +1,11 @@
-<tool id="redelacSticsSimulator" name="redelacSticsSimulator" version="1.0.5">
+<tool id="redelacSticsSimulator" name="redelacSticsSimulator" version="1.0.6">
   <description>to run sequences paralelly [Stics-10.0.0]</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:b0f76897e1ece4a91ecfc71617fec5ebd04e2bd4</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:0faa63e7838a2b86369026bf2e628842d7af9863</container>
   </requirements>
   <command detect_errors="aggressive">
     <![CDATA[ 
-              bash $__tool_directory__/redelacSticsSimulator.bash ${parallel} \${GALAXY_SLOTS:-4} ${Scenario} $__tool_directory__ ${Workspace} ${SuccessionPlan} ${SimulatedWorkspace} ${SimulationResults}
+              bash $__tool_directory__/redelacSticsSimulator.bash ${parallel} \${GALAXY_SLOTS:-4} ${Scenario} $__tool_directory__ ${Workspace} ${SuccessionPlan} ${SimulatedWorkspace} ${SimulationResults} ${compress}
      ]]>
   </command>
   <inputs>
@@ -13,6 +13,7 @@
     <param name="SuccessionPlan" type="data" format="csv" label="Select a plan of succession (csv)"/>
     <param name="Scenario" type="text" value="scenarioName" label="Scenario Name"/>
     <param name="parallel" type="boolean" checked="true" truevalue="parallel" falsevalue="sequential"/>
+    <param name="compress" type="boolean" checked="true" truevalue="-6" falsevalue="-0"/>
   </inputs>
   <outputs>
     <data format="zip" name="SimulatedWorkspace"
@@ -36,6 +37,19 @@
       </output>
     </test>
     <test>
+      <param name="compress" value="false" ftype="boolean" />
+      <param name="parallel" value="true" ftype="boolean" />
+      <param name="Workspace" value="input/rotx10.zip" ftype="zip" />
+      <param name="SuccessionPlan" value="input/listeUSMsExp10.csv" ftype="csv" />    
+      <output name="SimulationResults" ftype="zip" >
+	<assert_contents>
+	  <has_archive_member path="analyse_simulations_STICS\/1\/2\/report-2-806_1893-637_NGC1-scenarioName.csv">
+	    <has_text text="806_1893-637_NGC1-1-2-BT-NA-1973-BT" />
+	    	  </has_archive_member>
+	</assert_contents>	  
+      </output>
+    </test>
+    <test>
       <param name="parallel" value="false" ftype="boolean" />
       <param name="Workspace" value="input/rotx10.zip" ftype="zip" />
       <param name="SuccessionPlan" value="input/listeUSMsExp10.csv" ftype="csv" />