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comparison inSiliCow-run.sh @ 0:50112d3941d8 draft

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"planemo upload for repository https://forgemia.inra.fr/insilicow/insilicow-tool commit a01dd8fc54d5015e703722d7acb8db4b54b4a468"
author siwaa
date Mon, 07 Apr 2025 15:18:25 +0000
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-1:000000000000 0:50112d3941d8
1 #!/bin/bash
2
3 # Title: inSiliCow-run.sh
4 # Address: main/run
5 # Description: Launch simulations
6 # Authors: Olivier MARTIN ( https://orcid.org/0000-0001-7375-2850 )
7 # Pierre Blavy
8 # Contact: olivier.martin-mosar@inrae.fr
9 # Date: 2025
10 # Usage: inSiliCow-run.sh example_xx [out]
11 # example_xx is a folder in examples/
12 # out is the output folder, default ./out
13
14 clear
15
16 #--------------------------------------
17 #--- Colors for display in terminal ---
18 #--------------------------------------
19
20 # Set Bold High Intensity colors
21 R='\033[1;91m' # Red
22 B='\033[1;94m' # Blue
23 NC='\033[0m' # No Color
24
25 #Set BIP sound
26 BIP='\007'
27
28 # --- Opening message ---
29 echo -e ${B}"\n> Launching inSiliCow"${NC}
30
31 # -----------------------
32 # --- Input arguments ---
33 # -----------------------
34 #$1 is an example folder that exists in examples
35 #$2 is the output folder, must exists, default "./out"
36
37 if [ "$#" -le 0 ]; then
38 echo -e ${B}"\n>> Missing argument"
39 echo -e ">> Usage:"${NC}" inSilicow-run example_00 [out]"
40 echo -e ${B}"\n>> Aborted\n"${NC}
41 exit 1
42 fi
43
44 INPUT_DIR=$(realpath "examples/$1" )
45 OUTPUT_DIR=$(realpath ${2:-"./out"})
46 mkdir -p $OUTPUT_DIR
47
48
49 FARMER_LOG=$(realpath "examples/farmer-log.txt" )
50 SCRIPTS_DIR=$(realpath ./)
51 SCILAB=$(ls -drt $HOME/* | grep scilab- | tail -1)"/bin/scilab-cli"
52 INSILICOW=$(realpath ./../insilicow-linux)
53
54 CURRENT=`pwd`
55
56 # --------------------------
57 # --- Check things ---------
58 # --------------------------
59
60 #Input does'nt exists => return
61 if [ ! -d "$INPUT_DIR" ]; then
62 echo -e ${BIP}${R}"\n>> Input directory $INPUT_DIR does not exist\n";
63 echo -e ">> Aborted\n";
64 exit 1;
65 fi
66
67 #Output does'nt exists => return
68 #if [ ! -d "$OUTPUT_DIR" ]; then
69 # echo -e ${BIP}${R}"\n>> Output directory $OUTPUT_DIR does not exist\n";
70 # echo -e ">> Aborted\n";
71 # exit 1;
72 #fi
73
74 #inSiliCow binary does'nt exists => return
75 if [ ! -e "$INSILICOW" ]; then
76 echo -e ${BIP}${R}"\n>> inSiliCow binary $INSILICOW does not exist\n";
77 echo -e ">> Aborted\n";
78 exit 1;
79 fi
80
81 # -----------------------
82 # --- Output ------------
83 # -----------------------
84
85 #Get current date to name output folder
86 d=`date "+%Y%m%d_%H%M%S_%N"`
87 OUT_JOB="$OUTPUT_DIR/job-$d"
88 ZIP_FILE=$(realpath "$OUTPUT_DIR/simulations-$d.zip" )
89
90 # ------------------------------
91 # --- Print input and output ---
92 # ------------------------------
93
94 echo -e ${B}"\n>> Pathways:"
95 echo -e " Input:\t$INPUT_DIR";
96 echo -e " Output:\t$OUT_JOB";
97 echo -e " Scilab:\t$SCILAB";
98 echo -e " inSiliCow:\t$INSILICOW\n"${NC};
99
100
101 # ---------------------------------
102 # --- Make output folders ---------
103 # ---------------------------------
104 mkdir -p "$OUT_JOB/in";
105 mkdir -p "$OUT_JOB/out";
106
107 # -------------------------------------
108 # --- check if scilab is responding ---
109 # -------------------------------------
110
111 #check-scilab.sci xxx creates a file called "xxx/scilab_is_ok"
112 rm -f "$OUTPUT_DIR/scilab_is_ok"
113
114 #"$SCILAB" -f "$SCRIPTS_DIR/check-scilab.sci" -nwni -quit -args "$OUTPUT_DIR";
115
116 #if [ ! -f "$OUTPUT_DIR/scilab_is_ok" ]; then
117 # echo -e ${BIP}${R}"\n>> Scilab is not responding\n";
118 # echo -e ">> Aborted\n";
119 # exit 0;
120 #fi
121
122 rm "$OUTPUT_DIR/scilab_is_ok"
123
124 # --------------------------
125 # --- Run the jobs ---------
126 # --------------------------
127
128 # --- Track time ---
129 SECONDS=0;
130
131 #Format elapsed time
132 FormatSeconds () {
133 seconds="$1"
134 date -ud @${seconds} +"$(( seconds/3600/24 ))d %Hh %Mm %Ss" \
135 | sed -r 's/\b0([0-9])/\1/g; s/\b0(s|m|h|d)//g; s/ +/ /g; s/^ +//; s/ +$//; s/^$/0s/'
136 }
137
138 #copy input to $OUT_JOB/in
139 cp -r "$INPUT_DIR/"* "$OUT_JOB/in/"
140 cp "$FARMER_LOG" "$OUT_JOB/in/"
141
142 echo -e ${B}"\n>> Starting job $d\n"${NC}
143
144 # --------------
145 # --- explan ---
146 # --------------
147
148 #Create file explan-config.txt with right paths
149 cat > "$OUT_JOB/in/explan-config.txt" << EOF
150 explan{
151 IN_CPU = 4 #number of parallel jobs
152 IN_EXPLAN = $OUT_JOB/in/explan.txt
153 OUT_FOLDER = $OUT_JOB/out/
154 IN_FOLDER = $OUT_JOB/in/
155 IN_EXE = $INSILICOW
156 SCRIPT_FOLDER = $SCRIPTS_DIR
157 OUT_FOLDER = $OUT_JOB/sim
158 IN_SCILAB = $SCILAB
159 }
160 EOF
161
162
163 # Execute R script to launch simulations
164 echo -e ${B}"\n>> Starting simulation\n"${NC}
165 Rscript "$SCRIPTS_DIR/explan2.R" "$OUT_JOB/in/explan-config.txt"
166
167
168 # ZIP
169
170 #uncomment the block below to zip output
171
172 #rm -f "$ZIP_FILE"
173 #echo -e ${B}"\n>> Compress simulation to $ZIP_FILE \n"${NC}
174 #cd "$OUT_JOB" && \
175 #zip -rq9 "$ZIP_FILE" ./ -x out/sim_*/log_herd.txt && \
176 #cd "$CURRENT" && \
177 #rm -rf "$OUT_JOB"
178
179
180 # -----------------------------------
181 # --- display final message ---------
182 # -----------------------------------
183
184 echo -e ${B}"\n>> Job "$d" done in $(FormatSeconds $SECONDS)${NC}\n"
185