Mercurial > repos > siwaa > redelac_stics_t

annotate redelacSticsTool.bash @ 8:cbd23f8906db draft default tip

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 53d19ea66881dcd272711c98940626fa6bb58075"
author siwaa
date Thu, 24 Oct 2024 17:45:22 +0000
parents e0d592bb516e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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e0d592bb516e "planemo upload for repository https://forgemia.inra.fr/redelac commit 1b434482800e773a592b5fc6f472e7df465e91ce"
siwaa
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1 mkdir ./JavaSTICS-1.5.1-STICS-10.0.0 &&
e0d592bb516e "planemo upload for repository https://forgemia.inra.fr/redelac commit 1b434482800e773a592b5fc6f472e7df465e91ce"
siwaa
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2 cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/logs JavaSTICS-1.5.1-STICS-10.0.0 &&
e0d592bb516e "planemo upload for repository https://forgemia.inra.fr/redelac commit 1b434482800e773a592b5fc6f472e7df465e91ce"
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3 cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/config JavaSTICS-1.5.1-STICS-10.0.0 &&
e0d592bb516e "planemo upload for repository https://forgemia.inra.fr/redelac commit 1b434482800e773a592b5fc6f472e7df465e91ce"
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4 cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0/plant JavaSTICS-1.5.1-STICS-10.0.0 &&
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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5 rm -rf JavaSTICS-1.5.1-STICS-10.0.0/config &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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6 cp -r $4/config JavaSTICS-1.5.1-STICS-10.0.0 &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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7 unzip -q $5 -d TMP &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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8 export WSname=$(ls TMP) &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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9 mv TMP/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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10 cp ${17} JavaSTICS-1.5.1-STICS-10.0.0/WS/successionPlan.csv &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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11 cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_gen.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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12 cp JavaSTICS-1.5.1-STICS-10.0.0/config/param_newform.xml JavaSTICS-1.5.1-STICS-10.0.0/WS &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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13 /usr/bin/time -p -o ./bashlog unzip -q $6 -d TMPbis &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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14 echo "Step 0, time to unzip the Workspace:" &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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15 echo "====================================" &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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16 cat ./bashlog &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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17 echo "====================================" &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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18 mv TMPbis/*/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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19 cp $7 JavaSTICS-1.5.1-STICS-10.0.0/WS/USMs.csv &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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20 cp $8 JavaSTICS-1.5.1-STICS-10.0.0/WS/Tec.csv &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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21 cp $9 JavaSTICS-1.5.1-STICS-10.0.0/WS/Ini.csv &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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22 cp ${10} JavaSTICS-1.5.1-STICS-10.0.0/WS/Station.csv &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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23 cd JavaSTICS-1.5.1-STICS-10.0.0 &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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24 (if [ "${11}" != "noAdditionalPlantOrConfig" ];
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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25 then
8
cbd23f8906db "planemo upload for repository https://forgemia.inra.fr/redelac commit 53d19ea66881dcd272711c98940626fa6bb58075"
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26 unzip -q -o ${11} &&
cbd23f8906db "planemo upload for repository https://forgemia.inra.fr/redelac commit 53d19ea66881dcd272711c98940626fa6bb58075"
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27 cp -r plant WS &&
cbd23f8906db "planemo upload for repository https://forgemia.inra.fr/redelac commit 53d19ea66881dcd272711c98940626fa6bb58075"
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28 cp config/param_gen.xml WS &&
cbd23f8906db "planemo upload for repository https://forgemia.inra.fr/redelac commit 53d19ea66881dcd272711c98940626fa6bb58075"
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29 cp config/param_newform.xml WS
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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30 fi) &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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31 /usr/bin/time -p -o ./bashlog Rscript --verbose $4/redelacSticsTool.R $1 $2 $3 ${15} &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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32 echo "Step 1, time to run the R script:" &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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33 echo "=================================" &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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34 cat ./bashlog &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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35 echo "=================================" &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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36 cd WS &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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37 #/usr/bin/time -p -o ./bashlog zip ${13} -qq -r analyse_simulations_STICS analyse_simulations_STICS &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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38 /usr/bin/time -p -o ./bashlog 7z a -tzip -mx=1 -mmt=$3 analyse_simulations_STICS analyse_simulations_STICS &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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39 echo "Step 2, time to zip the results:" &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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40 echo "================================" &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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41 cat ./bashlog &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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42 echo "================================" &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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43 cp analyse_simulations_STICS.zip ${16} &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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44 rm -rf analyse_simulations_STICS &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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45 cd .. &&
2
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46 (if [ "${14}" != "yes" ];
aa575691d6f0 "planemo upload for repository https://forgemia.inra.fr/redelac commit 4176304bfa3f4beb3f49fb713b7dce81e93127f8"
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47 then
0
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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48 (cd WS && ls | grep -e '^[0-9]*\.[0-9]*$' | xargs -i rm {}) &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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49 mv WS $WSname &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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50 /usr/bin/time -p -o ./bashlog zip ${13} -y -q -r $WSname $WSname &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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51 echo "Step 2, time to zip the Workspace:" &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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52 echo "==================================" &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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53 cat ./bashlog &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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54 echo "==================================" &&
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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55 cp $WSname.zip ${12}
7f8f474a7bd7 "planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
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56 fi)