Mercurial > repos > siwaa > redelac_stics_s
changeset 2:ea8e91473dc8 draft
"planemo upload for repository https://forgemia.inra.fr/redelac/redelac-toolbox/-/tree/4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4/tools/REDELACSticsSimulator commit 4c3e6dc71284e3eecf1cfa8402aaf12dc49c1ee4-dirty"
| author | siwaa |
|---|---|
| date | Fri, 23 Jun 2023 10:17:27 +0000 |
| parents | be10e3fb6e64 |
| children | f262814e48a3 |
| files | parallelSticsRRotation-10.0.xml parallelSticsRRotation.R redelacSticsSimulator.R redelacSticsSimulator.xml stics_modulo version.txt |
| diffstat | 6 files changed, 137 insertions(+), 134 deletions(-) [+] |
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--- a/parallelSticsRRotation-10.0.xml Mon Jun 12 16:22:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ -<tool id="redelacSticsSimulator" name="redelacSticsSimulator" version="1.0.0"> - <description>to run sequences paralelly [Stics-10.0.0]</description> - <requirements> - <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics:10.0.0</container> - </requirements> - <command detect_errors="aggressive"> - <![CDATA[ - cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/JavaSTICS-1.5.1-STICS-10.0.0 . && - rm JavaSTICS-1.5.1-STICS-10.0.0/bin/stics_modulo && - cp $__tool_directory__/stics_modulo JavaSTICS-1.5.1-STICS-10.0.0/bin && - unzip ${WorkSpace} -d TMP && - export WSname=\$(ls TMP) && - mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS && - cp ${SuccessionPlan} JavaSTICS-1.5.1-STICS-10.0.0/WS/successionPlan.csv && - cd JavaSTICS-1.5.1-STICS-10.0.0 && - Rscript --verbose $__tool_directory__/parallelSticsRRotation.R && - mv WS \$WSname && - zip -r \$WSname \$WSname && - cp \$WSname.zip ${SimulatedWorkspace} && - cp results.RData ${SimulationResults} - ]]> - </command> - <inputs> - <param name="WorkSpace" type="data" format="zip" label="Select a stics Workspace(zip file)"/> - <param name="SuccessionPlan" type="data" format="csv" label="Select a plan of succession (csv)"/> - </inputs> - <outputs> - <data format="zip" name="SimulatedWorkspace" - label="Stics simulated Workspace"> - </data> - <data format="rdata" name="SimulationResults" - label="Stics simulations results"> - </data> - </outputs> - <tests> - </tests> - <help> -*The usage of this tool is restricted to the user of the stics_authorized group.* - -*To be granted, apply to the Project Stics Team and then request to SIWAA* - -Documentation -------------- -A tool to simulate stics rotation paralelly - -Credits -------- -- Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team -- Stics Site: https://www6.paca.inra.fr/stics_eng -- Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr -- Copyright: INRAE - </help> -</tool>
--- a/parallelSticsRRotation.R Mon Jun 12 16:22:04 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,81 +0,0 @@ -library(SticsRFiles) -library(SticsOnR) -library(parallel) -library(doParallel) -library(readxl) - -workspace <- paste0(getwd(), "/WS") -javastics_path <- getwd() -default_config_path <- paste0(javastics_path, "/config") - -# copy of the var.mod and rap.mod into the config folder -# generalizing maybe should be inside a config folder - -#file.copy(from = file.path(workspace, "var.mod"), -# to = file.path(default_config_path, "var.mod"), -# overwrite = TRUE) -#file.copy(from = file.path(workspace, "rap.mod"), -# to = file.path(default_config_path, "rap.mod"), -# overwrite = TRUE) - -txt_path <- paste0(getwd(), "/WS/txt_files") -#dir.create(txt_path,recursive = T) - -#gen_usms_xml2txt(javastics = javastics_path, -# workspace = workspace, -# out_dir = txt_path, -# check = FALSE) - -print("==================================") - -print(paste0("Cores=", detectCores())) -print(paste0("javastics=", javastics_path)) -print(paste0("ws=", workspace)) -print(paste0("out_dir=", txt_path)) - -print("==================================") - - -# List of successive USMs -successive_usms_file <- ("successionPlan.csv") -successive_usms_tab <- read.csv(file = file.path(workspace, successive_usms_file), sep =";") - -no_cores <- detectCores() - 1 -no_cores <- 10 -cl <- makeCluster(no_cores) -registerDoParallel(cl) - -result <- foreach(i=1:nrow(successive_usms_tab), - .packages = c("SticsRFiles", "SticsOnR") ) %dopar% { - - - print(paste("coucou ", i)) - nusms <- as.numeric(successive_usms_tab[i,2]) - print(paste0("coco ", nusms)) - - vec <- as.character(successive_usms_tab[i,c(3:(2+nusms))]) - - list_successive_usms <- list(vec) - - sim_options <- stics_wrapper_options(javastics = javastics_path, - stics_exe = paste0(javastics_path,"/bin/stics_modulo"), - workspace = txt_path, - verbose = TRUE, - successive = list_successive_usms) - list_usms <- vec - - stics_wrapper(model_options = sim_options, situation = list_usms) - } - -stopCluster(cl) - -for (i in 1:nrow(successive_usms_tab)) { #i=1 - if (i == 1) { - simPCP <- result[[i]] - } else { - simPCP$sim_list <- c(simPCP$sim_list, result[[i]]$sim_list) - } - -} - -save(simPCP, file = "results.RData")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/redelacSticsSimulator.R Fri Jun 23 10:17:27 2023 +0000 @@ -0,0 +1,81 @@ +library(SticsRFiles) +library(SticsOnR) +library(parallel) +library(doParallel) +library(readxl) + +workspace <- paste0(getwd(), "/WS") +javastics_path <- getwd() +default_config_path <- paste0(javastics_path, "/config") + +# copy of the var.mod and rap.mod into the config folder +# generalizing maybe should be inside a config folder + +#file.copy(from = file.path(workspace, "var.mod"), +# to = file.path(default_config_path, "var.mod"), +# overwrite = TRUE) +#file.copy(from = file.path(workspace, "rap.mod"), +# to = file.path(default_config_path, "rap.mod"), +# overwrite = TRUE) + +txt_path <- paste0(getwd(), "/WS/txt_files") +#dir.create(txt_path,recursive = T) + +#gen_usms_xml2txt(javastics = javastics_path, +# workspace = workspace, +# out_dir = txt_path, +# check = FALSE) + +print("==================================") + +print(paste0("Cores=", detectCores())) +print(paste0("javastics=", javastics_path)) +print(paste0("ws=", workspace)) +print(paste0("out_dir=", txt_path)) + +print("==================================") + + +# List of successive USMs +successive_usms_file <- ("successionPlan.csv") +successive_usms_tab <- read.csv(file = file.path(workspace, successive_usms_file), sep =";") + +no_cores <- detectCores() - 1 +#no_cores <- 10 +cl <- makeCluster(no_cores) +registerDoParallel(cl) + +result <- foreach(i=1:nrow(successive_usms_tab), + .packages = c("SticsRFiles", "SticsOnR") ) %dopar% { + + + print(paste("coucou ", i)) + nusms <- as.numeric(successive_usms_tab[i,2]) + print(paste0("coco ", nusms)) + + vec <- as.character(successive_usms_tab[i,c(3:(2+nusms))]) + + list_successive_usms <- list(vec) + + sim_options <- stics_wrapper_options(javastics = javastics_path, + stics_exe = paste0(javastics_path,"/bin/stics_modulo"), + workspace = txt_path, + verbose = TRUE, + successive = list_successive_usms) + list_usms <- vec + + stics_wrapper(model_options = sim_options, situation = list_usms) + } + +stopCluster(cl) + +for (i in 1:nrow(successive_usms_tab)) { #i=1 + if (i == 1) { + simPCP <- result[[i]] + } else { + simPCP$sim_list <- c(simPCP$sim_list, result[[i]]$sim_list) + } + +} + +save(simPCP, file = "results.RData")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/redelacSticsSimulator.xml Fri Jun 23 10:17:27 2023 +0000 @@ -0,0 +1,54 @@ +<tool id="redelacSticsSimulator" name="redelacSticsSimulator" version="1.0.1"> + <description>to run sequences paralelly [Stics-10.0.0]</description> + <requirements> + <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics:10.0.0</container> + </requirements> + <command detect_errors="aggressive"> + <![CDATA[ + cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/JavaSTICS-1.5.1-STICS-10.0.0 . && + rm JavaSTICS-1.5.1-STICS-10.0.0/bin/stics_modulo && + cp $__tool_directory__/stics_modulo JavaSTICS-1.5.1-STICS-10.0.0/bin && + unzip -qq ${WorkSpace} -d TMP && + export WSname=\$(ls TMP) && + mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS && + cp ${SuccessionPlan} JavaSTICS-1.5.1-STICS-10.0.0/WS/successionPlan.csv && + cd JavaSTICS-1.5.1-STICS-10.0.0 && + Rscript --verbose $__tool_directory__/redelacSticsSimulator.R \${GALAXY_SLOTS:-2} && + mv WS \$WSname && + zip -qq -r \$WSname \$WSname && + cp \$WSname.zip ${SimulatedWorkspace} && + cp results.RData ${SimulationResults} + ]]> + </command> + <inputs> + <param name="WorkSpace" type="data" format="zip" label="Select a stics Workspace(zip file)"/> + <param name="SuccessionPlan" type="data" format="csv" label="Select a plan of succession (csv)"/> + <param name="Tag" type="text" value="" label="Outputs tag"/> + </inputs> + <outputs> + <data format="zip" name="SimulatedWorkspace" + label="SticsSimulatedWorkspace${Tag}"> + </data> + <data format="rdata" name="SimulationResults" + label="SticsOnResults${Tag}"> + </data> + </outputs> + <tests> + </tests> + <help> +*The usage of this tool is restricted to the user of the stics_authorized group.* + +*To be granted, apply to the Project Stics Team and then request to SIWAA* + +Documentation +------------- +A tool to simulate stics rotation paralelly + +Credits +------- +- Wrapped Tool Author: https://www6.paca.inrae.fr/stics_eng/About-us/Project-Stics-Team +- Stics Site: https://www6.paca.inra.fr/stics_eng +- Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr +- Copyright: INRAE + </help> +</tool>