Mercurial > repos > davidvanzessen > shm_csr
comparison wrapper.sh @ 95:d63eff357515 draft
planemo upload commit d96a736dcd6da34137f79861fbc6369716c332f1
author | rhpvorderman |
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date | Mon, 27 Mar 2023 13:11:53 +0000 |
parents | 84e9e5c8c101 |
children | 385dea3c6cb5 |
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94:84e9e5c8c101 | 95:d63eff357515 |
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21 filter_unique=${17} | 21 filter_unique=${17} |
22 filter_unique_count=${18} | 22 filter_unique_count=${18} |
23 class_filter=${19} | 23 class_filter=${19} |
24 empty_region_filter=${20} | 24 empty_region_filter=${20} |
25 fast=${21} | 25 fast=${21} |
26 | 26 BASENAME=$(basename "$input") |
27 BASENAME=$(basename $input) | 27 # Cut off .txz or .tgz suffix and also replace spaces with underscores. |
28 # Cut off .txz or .tgz suffix | |
29 NEW_IMGT_PREFIX="new_IMGT_${BASENAME%.*}" | 28 NEW_IMGT_PREFIX="new_IMGT_${BASENAME%.*}" |
29 NEW_IMGT_PREFIX=${NEW_IMGT_PREFIX// /_} | |
30 | 30 |
31 #exec 5> debug_output.txt | 31 #exec 5> debug_output.txt |
32 #BASH_XTRACEFD="5" | 32 #BASH_XTRACEFD="5" |
33 ## Busybox date does not support '+%s.%N'. So use a custom program. Can be | 33 ## Busybox date does not support '+%s.%N'. So use a custom program. Can be |
34 ## Compiled with cc -Os show_time_as_float.c -o show_time_as_float | 34 ## Compiled with cc -Os show_time_as_float.c -o show_time_as_float |
42 echo "---------------- read parameters ----------------" | 42 echo "---------------- read parameters ----------------" |
43 echo "---------------- read parameters ----------------<br />" > $log | 43 echo "---------------- read parameters ----------------<br />" > $log |
44 | 44 |
45 echo "unpacking IMGT file" | 45 echo "unpacking IMGT file" |
46 | 46 |
47 type="`file -L $input`" | 47 type="$(file -L "$input")" |
48 if [[ "$type" == *"Zip archive"* ]] ; then | 48 if [[ "$type" == *"Zip archive"* ]] ; then |
49 echo "Zip archive" | 49 echo "Zip archive" |
50 echo "unzip $input -d $PWD/files/" | 50 echo "unzip $input -d $PWD/files/" |
51 unzip $input -d $PWD/files/ | 51 unzip "$input" -d $PWD/files/ |
52 elif [[ "$type" == *"XZ compressed data"* ]] ; then | 52 elif [[ "$type" == *"XZ compressed data"* ]] ; then |
53 echo "ZX archive" | 53 echo "ZX archive" |
54 echo "tar -xJf $input -C $PWD/files/" | 54 echo "tar -xJf "$input" -C $PWD/files/" |
55 mkdir -p "$PWD/files/$title" | 55 mkdir -p "$PWD/files/$title" |
56 tar -xJf $input -C "$PWD/files/$title" | 56 tar -xJf "$input" -C "$PWD/files/$title" |
57 else | 57 else |
58 echo "Unrecognized format $type" | 58 echo "Unrecognized format $type" |
59 echo "Unrecognized format $type" > $log | 59 echo "Unrecognized format $type" > $log |
60 exit 1 | 60 exit 1 |
61 fi | 61 fi |
110 ${empty_region_filter} | 110 ${empty_region_filter} |
111 | 111 |
112 echo "---------------- creating new IMGT zips ----------------" | 112 echo "---------------- creating new IMGT zips ----------------" |
113 echo "---------------- creating new IMGT zips ----------------<br />" >> $log | 113 echo "---------------- creating new IMGT zips ----------------<br />" >> $log |
114 | 114 |
115 python $dir/split_imgt_file.py --outdir $outdir $input $outdir/merged.txt \ | 115 python $dir/split_imgt_file.py --outdir $outdir "$input" $outdir/merged.txt \ |
116 --prefix "${NEW_IMGT_PREFIX}" \ | 116 --prefix "${NEW_IMGT_PREFIX}" \ |
117 - IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE | 117 - IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE |
118 | 118 |
119 | 119 |
120 echo "---------------- shm_csr.r ----------------" | 120 echo "---------------- shm_csr.r ----------------" |