Mercurial > repos > siwaa > redelac_stics_g

annotate redelacSticsInputGenerator.bash @ 13:3db1f57029a7 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 4a2264991516b494ed11d1a7d5260ba543696a04"
author siwaa
date Fri, 27 Oct 2023 09:17:06 +0000
parents f707c2fb725b
children 812bb8097dac
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2a6d7d053ba7 "planemo upload for repository https://forgemia.inra.fr/redelac commit adcac73e150f1f821b4b7f7673a490dc0fadc936"
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1 cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0 . &&
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2 rm -rf JavaSTICS-1.5.1-STICS-10.0.0/config &&
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3 cp -r $4/config JavaSTICS-1.5.1-STICS-10.0.0 &&
2a6d7d053ba7 "planemo upload for repository https://forgemia.inra.fr/redelac commit adcac73e150f1f821b4b7f7673a490dc0fadc936"
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4 unzip -q $5 -d TMP &&
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5 export WSname=$(ls TMP) &&
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6 mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
4f8d87b9c246 "planemo upload for repository https://forgemia.inra.fr/redelac commit b3a95e69b8c2496ff3ec12c854404798d8bc55b1"
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7 cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_gen.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
4f8d87b9c246 "planemo upload for repository https://forgemia.inra.fr/redelac commit b3a95e69b8c2496ff3ec12c854404798d8bc55b1"
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8 cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_newform.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
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9 /usr/bin/time -p -o ./bashlog unzip -q $6 -d TMPbis &&
f707c2fb725b "planemo upload for repository https://forgemia.inra.fr/redelac commit af2d1fcb63a2ae897e02f11e82cc76c4f6e8ca5e"
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10 echo "Step 0, time to unzip the Workspace:" &&
f707c2fb725b "planemo upload for repository https://forgemia.inra.fr/redelac commit af2d1fcb63a2ae897e02f11e82cc76c4f6e8ca5e"
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11 echo "====================================" &&
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12 cat ./bashlog &&
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13 echo "====================================" &&
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14 mv TMPbis/*/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
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15 cp $7 JavaSTICS-1.5.1-STICS-10.0.0/WS/USMs.csv &&
2a6d7d053ba7 "planemo upload for repository https://forgemia.inra.fr/redelac commit adcac73e150f1f821b4b7f7673a490dc0fadc936"
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16 cp $8 JavaSTICS-1.5.1-STICS-10.0.0/WS/Tec.csv &&
2a6d7d053ba7 "planemo upload for repository https://forgemia.inra.fr/redelac commit adcac73e150f1f821b4b7f7673a490dc0fadc936"
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17 cp $9 JavaSTICS-1.5.1-STICS-10.0.0/WS/Ini.csv &&
2a6d7d053ba7 "planemo upload for repository https://forgemia.inra.fr/redelac commit adcac73e150f1f821b4b7f7673a490dc0fadc936"
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18 cp ${10} JavaSTICS-1.5.1-STICS-10.0.0/WS/Station.csv &&
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19 cd JavaSTICS-1.5.1-STICS-10.0.0 &&
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20 if [[ "$11" != "noAdditionalPlantOrConfig" ]]
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21 then
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22 unzip -o ${10}
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23 fi
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24 /usr/bin/time -p -o ./bashlog Rscript --verbose $4/redelacSticsInputGenerator.R $1 $2 $3 &&
f707c2fb725b "planemo upload for repository https://forgemia.inra.fr/redelac commit af2d1fcb63a2ae897e02f11e82cc76c4f6e8ca5e"
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25 echo "Step 1, time to run the R script:" &&
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26 echo "=================================" &&
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27 cat ./bashlog &&
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28 echo "=================================" &&
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29 rm WS/1* &&
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30 mv WS $WSname &&
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31 /usr/bin/time -p -o ./bashlog zip ${13} -q -r $WSname $WSname &&
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32 echo "Step 2, time to zip the Workspace:" &&
f707c2fb725b "planemo upload for repository https://forgemia.inra.fr/redelac commit af2d1fcb63a2ae897e02f11e82cc76c4f6e8ca5e"
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33 echo "==================================" &&
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34 cat ./bashlog &&
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35 echo "==================================" &&
f707c2fb725b "planemo upload for repository https://forgemia.inra.fr/redelac commit af2d1fcb63a2ae897e02f11e82cc76c4f6e8ca5e"
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36 cp $WSname.zip ${12}