Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 83:729738462297 draft

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"planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
author rhpvorderman
date Wed, 15 Sep 2021 12:24:06 +0000
parents b6f9a640e098
children 4db34e32dd47
comparison
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82:a103134ee6e0 83:729738462297
1 #!/bin/bash 1 #!/usr/bin/env bash
2 #set -e 2 set -e -o pipefail
3 dir="$(cd "$(dirname "$0")" && pwd)" 3 dir="$(cd "$(dirname "$0")" && pwd)"
4 input=$1 4 input=$1
5 method=$2 5 method=$2
6 log=$3 #becomes the main html page at the end 6 log=$3 #becomes the main html page at the end
7 outdir=$4 7 outdir=$4
20 filter_unique_count=${16} 20 filter_unique_count=${16}
21 class_filter=${17} 21 class_filter=${17}
22 empty_region_filter=${18} 22 empty_region_filter=${18}
23 fast=${19} 23 fast=${19}
24 24
25 mkdir $outdir 25 #exec 5> debug_output.txt
26 #BASH_XTRACEFD="5"
27 #PS4='$(date +%s.%N) $LINENO: '
28 #set -x
29
30 mkdir -p $outdir
26 31
27 tar -xzf $dir/style.tar.gz -C $outdir 32 tar -xzf $dir/style.tar.gz -C $outdir
28 33
29 echo "---------------- read parameters ----------------" 34 echo "---------------- read parameters ----------------"
30 echo "---------------- read parameters ----------------<br />" > $log 35 echo "---------------- read parameters ----------------<br />" > $log
445 450
446 echo "---------------- baseline ----------------" 451 echo "---------------- baseline ----------------"
447 echo "---------------- baseline ----------------<br />" >> $log 452 echo "---------------- baseline ----------------<br />" >> $log
448 tmp="$PWD" 453 tmp="$PWD"
449 454
450 mkdir $outdir/baseline 455 mkdir -p $outdir/baseline
451 456
452 echo "<center><h1>BASELINe</h1>" >> $output 457 echo "<center><h1>BASELINe</h1>" >> $output
453 header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)" 458 header_substring="Based on CDR1, FR2, CDR2, FR3 (27:27:38:55:65:104:-)"
454 459
455 baseline_boundaries="27:27:38:55:65:104:-" 460 baseline_boundaries="27:27:38:55:65:104:-"
555 560
556 if [[ "$fast" == "no" ]] ; then 561 if [[ "$fast" == "no" ]] ; then
557 562
558 echo "---------------- change-o MakeDB ----------------" 563 echo "---------------- change-o MakeDB ----------------"
559 564
560 mkdir $outdir/change_o 565 mkdir -p $outdir/change_o
561 566
562 tmp="$PWD" 567 tmp="$PWD"
563 568
564 cd $outdir/change_o 569 cd $outdir/change_o
565 570