Mercurial > repos > siwaa > redelac_stics_g

annotate redelacSticsInputGenerator.bash @ 9:2a6d7d053ba7 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit adcac73e150f1f821b4b7f7673a490dc0fadc936"
author siwaa
date Mon, 25 Sep 2023 16:25:51 +0000
parents 0625e6a639ea
children f707c2fb725b
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"
siwaa
parents: 8
diff changeset
1 cp -r /home/rstudio/JavaSTICS-1.5.1-STICS-10.0.0 . &&
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4f8d87b9c246 "planemo upload for repository https://forgemia.inra.fr/redelac commit b3a95e69b8c2496ff3ec12c854404798d8bc55b1"
siwaa
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2 rm -rf JavaSTICS-1.5.1-STICS-10.0.0/config &&
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2a6d7d053ba7 "planemo upload for repository https://forgemia.inra.fr/redelac commit adcac73e150f1f821b4b7f7673a490dc0fadc936"
siwaa
parents: 8
diff changeset
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"
siwaa
parents: 8
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4 unzip -q $5 -d TMP &&
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4f8d87b9c246 "planemo upload for repository https://forgemia.inra.fr/redelac commit b3a95e69b8c2496ff3ec12c854404798d8bc55b1"
siwaa
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5 export WSname=$(ls TMP) &&
4f8d87b9c246 "planemo upload for repository https://forgemia.inra.fr/redelac commit b3a95e69b8c2496ff3ec12c854404798d8bc55b1"
siwaa
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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"
siwaa
parents:
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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"
siwaa
parents:
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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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2a6d7d053ba7 "planemo upload for repository https://forgemia.inra.fr/redelac commit adcac73e150f1f821b4b7f7673a490dc0fadc936"
siwaa
parents: 8
diff changeset
9 unzip -q $6 -d TMPbis &&
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4f8d87b9c246 "planemo upload for repository https://forgemia.inra.fr/redelac commit b3a95e69b8c2496ff3ec12c854404798d8bc55b1"
siwaa
parents:
diff changeset
10 mv TMPbis/*/* JavaSTICS-1.5.1-STICS-10.0.0/WS &&
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2a6d7d053ba7 "planemo upload for repository https://forgemia.inra.fr/redelac commit adcac73e150f1f821b4b7f7673a490dc0fadc936"
siwaa
parents: 8
diff changeset
11 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"
siwaa
parents: 8
diff changeset
12 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"
siwaa
parents: 8
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13 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"
siwaa
parents: 8
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14 cp ${10} JavaSTICS-1.5.1-STICS-10.0.0/WS/Station.csv &&
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4f8d87b9c246 "planemo upload for repository https://forgemia.inra.fr/redelac commit b3a95e69b8c2496ff3ec12c854404798d8bc55b1"
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15 cd JavaSTICS-1.5.1-STICS-10.0.0 &&
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siwaa
parents: 8
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16 Rscript --verbose $4/redelacSticsInputGenerator.R $1 $2 $3 &&
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siwaa
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17 rm WS/1* &&
4f8d87b9c246 "planemo upload for repository https://forgemia.inra.fr/redelac commit b3a95e69b8c2496ff3ec12c854404798d8bc55b1"
siwaa
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18 mv WS $WSname &&
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fb6f7d60508d "planemo upload for repository https://forgemia.inra.fr/redelac commit d1c69d78e9ccfe06ceb7609dce59b438cd94d9d8"
siwaa
parents: 5
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19 zip -q -r $WSname $WSname &&
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2a6d7d053ba7 "planemo upload for repository https://forgemia.inra.fr/redelac commit adcac73e150f1f821b4b7f7673a490dc0fadc936"
siwaa
parents: 8
diff changeset
20 cp $WSname.zip ${11}