Mercurial > repos > siwaa > redelac_stics_t
changeset 24:0e673be917e3 draft
"planemo upload for repository https://forgemia.inra.fr/redelac commit 596ce5faab821d6dcaf17fd56e002adc5be472fc"
| author | siwaa |
|---|---|
| date | Tue, 01 Sep 2026 07:35:51 +0000 |
| parents | 3b44cb0a1e76 |
| children | 6839c9c8555e |
| files | redelacSticsTool.bash redelacSticsTool.xml |
| diffstat | 2 files changed, 25 insertions(+), 3 deletions(-) [+] |
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--- a/redelacSticsTool.bash Wed Aug 19 14:35:50 2026 +0000 +++ b/redelacSticsTool.bash Tue Sep 01 07:35:51 2026 +0000 @@ -34,6 +34,11 @@ cat ./bashlog && echo "=================================" && cd WS && +(if [ "${19}" != "ko" ]; + then + (aws s3 cp analyse_simulations_STICS "${20}" --recursive --endpoint-url "${S3_ENDPOINT}") + else +( #/usr/bin/time -p -o ./bashlog zip ${13} -qq -r analyse_simulations_STICS analyse_simulations_STICS && /usr/bin/time -p -o ./bashlog 7z a -tzip -mx=1 -mmt=$3 analyse_simulations_STICS analyse_simulations_STICS && echo "Step 2, time to zip the results:" && @@ -42,7 +47,8 @@ echo "================================" && cp analyse_simulations_STICS.zip ${16} && rm -rf analyse_simulations_STICS && -cd .. && +cd ..) +fi) && (if [ "${14}" != "yes" ]; then (cd WS && ls | grep -e '^[0-9]*\.[0-9]*$' | xargs -i rm {}) &&
--- a/redelacSticsTool.xml Wed Aug 19 14:35:50 2026 +0000 +++ b/redelacSticsTool.xml Tue Sep 01 07:35:51 2026 +0000 @@ -1,4 +1,4 @@ -<tool id="redelacSticsTool" name="redelacSticsTool" version="1.0.25"> +<tool id="redelacSticsTool" name="redelacSticsTool" version="1.0.26"> <description>to run Stics for REDELAC</description> <requirements> <container type="singularity">docker://registry.forge.inrae.fr/redelac/redelac-toolbox/sticsrpacks:5337507635242b3ad0f3559a1a6b666512ecf002 @@ -6,6 +6,12 @@ </requirements> <command detect_errors="aggressive"> <![CDATA[ + env && + curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" && + unzip awscliv2.zip && + ./aws/install --update -i ~/.local/aws-cli -b ~/.local/bin && + export PATH=\${HOME}/.local/bin:\${PATH} && + aws --version && #if $additional: additional=${additional} && #else @@ -16,7 +22,7 @@ #else parallel=sequential && #end if - bash $__tool_directory__/redelacSticsTool.bash ${REDELAC.optim} \${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} \${additional} ${GeneratedWorkspace} ${compress} ${outputsOnly} ${Scenario} ${SimulationResults} ${SuccessionPlan} ${outpuType} + bash $__tool_directory__/redelacSticsTool.bash ${REDELAC.optim} \${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} \${additional} ${GeneratedWorkspace} ${compress} ${outputsOnly} ${Scenario} ${SimulationResults} ${SuccessionPlan} ${outpuType} ${S3.S3} s3://${Bucket}/${objectPath} ]]> </command> <inputs> @@ -44,10 +50,20 @@ <option value="rds+csv">rds+csv</option> <option value="both" selected="true">both</option> </param> + <conditional name="S3"> + <param name="S3" type="boolean" checked="true" truevalue="ok" falsevalue="ko" label="To store directly on a Tenant"/> + <when value="ok"> + <param name="objectPath" type="text" value="Simulations-stics/sous-territoires/PDF/ICHEC-EC-EARTH" label="a path to the object"/> + <param name="Bucket" type="text" value="dairyfit-donnees-produites" label="the bucket where to store"/> + </when> + <when value="ko"> + </when> + </conditional> </inputs> <outputs> <data format="zip" name="SimulationResults" label="SticsOnResults"> + <filter>S3.S3 == False</filter> </data> <data format="zip" name="GeneratedWorkspace" label="GeneratedWorkspace$">