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annotate inSiliCow-post.sh @ 4:7d099adc5236 draft default tip

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"planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit 1d3f800321015b530cc4ff416bcc391896297604"
author siwaa
date Wed, 27 Aug 2025 10:17:55 +0000
parents 50112d3941d8
children
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50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
siwaa
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1 #!/bin/sh
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
siwaa
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50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
siwaa
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3 echo "IN_EXPLAN=$IN_EXPLAN" #
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
siwaa
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4 echo "OUT_FOLDER=$OUT_FOLDER" #
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
siwaa
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5 echo "IN_FOLDER=$IN_FOLDER" #
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
siwaa
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6 echo "IN_EXE=$IN_EXE" #
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
siwaa
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7 echo "SCRIPT_FOLDER=$SCRIPT_FOLDER" #
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
siwaa
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8 echo "OUT_FOLDER=$OUT_FOLDER" #
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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9 echo "IN_SCILAB=$IN_SCILAB" #
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
siwaa
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10 echo "OUT_SIM=$OUT_SIM" #
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
siwaa
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11 echo "SIM_ID=$SIM_ID" #
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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13 HERE=$(realpath ./ )
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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15 echo "$OUT_SIM BEGIN" &&\
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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16 cp "$IN_FOLDER/farmer-log.txt" "$OUT_SIM" && \
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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17 cd "$OUT_SIM" && \
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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18 "$IN_EXE" farmer.txt > log.txt && \
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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19 mkdir cows && \
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
siwaa
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20 Rscript "$SCRIPT_FOLDER/cowcut.R" "./" "cows/" && \
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
siwaa
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21 MESA_GL_VERSION_OVERRIDE=3.0 "$IN_SCILAB" -f "$SCRIPT_FOLDER/inSiliCow-abby.sci" -nwni -quit -args "$OUT_SIM" "$OUT_SIM" "$PL_PREFIX$SIM_ID$PL_SUFFIX" && \
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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22 echo "$OUT_SIM OK"
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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24 #--- ZIP individual sim forlers ---
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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25 #cd "$OUT_FOLDER" && \
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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26 #zip -rmq9 "$SIM_ID.zip" "$SIM_ID" ;
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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27 #cd "$HERE";
50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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50112d3941d8 "planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
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