Mercurial > repos > siwaa > redelac_stics_g
changeset 17:4d0807472ad3 draft default tip
"planemo upload for repository https://forgemia.inra.fr/redelac commit 9c5802d9b947f1e59bd5df610ebe5dfc89745be6"
| author | siwaa |
|---|---|
| date | Tue, 23 Jan 2024 18:51:34 +0000 |
| parents | f2fe11a20371 |
| children | |
| files | redelacSticsInputGenerator.R redelacSticsInputGenerator.bash redelacSticsInputGenerator.xml |
| diffstat | 3 files changed, 10 insertions(+), 8 deletions(-) [+] |
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--- a/redelacSticsInputGenerator.R Mon Jan 22 15:15:07 2024 +0000 +++ b/redelacSticsInputGenerator.R Tue Jan 23 18:51:34 2024 +0000 @@ -78,8 +78,10 @@ if (parallel) { doFuture::registerDoFuture() - - future::plan(multicore, workers = nbSlots) + future::plan(multisession, workers = nbSlots) + `%dordopar%` <- `%dofuture%` +} else { + `%dordopar%` <- `%do%` } beforeGenXmlTime <- Sys.time() @@ -93,7 +95,7 @@ ids <- seq(1, nbUSMs, chunckSize) foreach (i = ids, - .options.future = list(packages = c("foreach", "SticsRFiles"))) %dofuture% { + .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% { gen_usms_xml(file = file.path(workspace, paste0("usms__", i, ".xml")), param_df = usms_param[i:min(i + chunckSize - 1, nbUSMs),]) } @@ -106,7 +108,7 @@ beforeGenTxtTime <- Sys.time() foreach (i = ids, - .options.future = list(packages = c("foreach", "SticsRFiles"))) %dofuture% { + .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% { gen_usms_xml2txt( javastics = javastics_path, workspace = workspace,
--- a/redelacSticsInputGenerator.bash Mon Jan 22 15:15:07 2024 +0000 +++ b/redelacSticsInputGenerator.bash Tue Jan 23 18:51:34 2024 +0000 @@ -27,9 +27,9 @@ echo "=================================" && cat ./bashlog && echo "=================================" && -rm WS/1* && +(cd WS && ls | grep -e '^[0-9]*\.[0-9]*$' | xargs -i rm {}) && mv WS $WSname && -/usr/bin/time -p -o ./bashlog zip ${13} -q -r $WSname $WSname && +/usr/bin/time -p -o ./bashlog zip ${13} -y -q -r $WSname $WSname && echo "Step 2, time to zip the Workspace:" && echo "==================================" && cat ./bashlog &&
--- a/redelacSticsInputGenerator.xml Mon Jan 22 15:15:07 2024 +0000 +++ b/redelacSticsInputGenerator.xml Tue Jan 23 18:51:34 2024 +0000 @@ -1,7 +1,7 @@ -<tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.9"> +<tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.10"> <description>to run generate Stics Inputs for REDELAC</description> <requirements> - <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:34ec8256987dc39507f0679d110c6306b00d5890</container> + <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:5d8a06fbf5783ca65fba694dbeb5d2749020c36d</container> </requirements> <command detect_errors="aggressive"> <![CDATA[