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comparison ceas_wrapper.sh @ 3:82df5af2995f draft

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Renamed from "ceasbw..." to "ceas...".
author pjbriggs
date Wed, 22 Apr 2015 05:34:06 -0400
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children 4e2883bb058d
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2:695d61decd06 3:82df5af2995f
1 #!/bin/sh -e
2 #
3 # Wrapper script to run CEAS as a Galaxy tool
4 #
5 # This runs the Cistrome versions of CEAS, which provides two executables:
6 # - ceas (same as the "official" version)
7 # - ceasBW (modified version that accepts a bigwig file as input)
8 #
9 # Usage: ceas_wrapper.sh $BED_IN $GDB_IN $EXTRA_BED_IN $LOG_OUT $PDF_OUT $XLS_OUT $DBKEY
10 #
11 # Process command line
12 echo $*
13 BED_IN=$1
14 GDB_IN=$2
15 EXTRA_BED_IN=$3
16 LOG_OUT=$4
17 PDF_OUT=$5
18 XLS_OUT=$6
19 #
20 # Collect remaining args
21 CEAS=ceas
22 OPTIONS=
23 while [ ! -z "$7" ] ; do
24 if [ "$7" == "--bigwig" ] ; then
25 CEAS=ceasBW
26 fi
27 if [ "$7" == "--length" ] ; then
28 chrom_sizes=$8
29 if [ ! -f "$chrom_sizes" ] ; then
30 echo "ERROR no file $chrom_sizes" >&2
31 echo "Please update your Galaxy instance to include this file"
32 exit 1
33 fi
34 fi
35 OPTIONS="$OPTIONS $7"
36 shift
37 done
38 #
39 # Convenience variables for local files
40 base_name="ceas"
41 log_file=${base_name}.log
42 r_script=${base_name}.R
43 pdf_report=${base_name}.pdf
44 xls_file=${base_name}.xls
45 #
46 # Get CEAS version
47 echo Running $CEAS
48 $CEAS --version >$log_file 2>/dev/null
49 #
50 # Construct and run CEAS command line
51 ceas_cmd="$CEAS --name $base_name $OPTIONS -g $GDB_IN -b $BED_IN"
52 if [ "$EXTRA_BED_IN" != "None" ] ; then
53 ceas_cmd="$ceas_cmd -e $EXTRA_BED_IN"
54 fi
55 echo "Running $ceas_cmd"
56 $ceas_cmd >>$log_file 2>&1
57 #
58 # Move outputs to final destination
59 if [ -e $log_file ] ; then
60 echo "Moving $log_file to $LOG_OUT"
61 /bin/mv $log_file $LOG_OUT
62 else
63 echo ERROR failed to make log file >&2
64 exit 1
65 fi
66 if [ -e $xls_file ] ; then
67 echo "Moving $xls_file to $XLS_OUT"
68 /bin/mv $xls_file $XLS_OUT
69 else
70 echo ERROR failed to generate XLS file >&2
71 exit 1
72 fi
73 #
74 # Run the R script to generate the PDF report
75 if [ -e $r_script ] ; then
76 echo "Running $r_script to generate $pdf_report"
77 R --vanilla < $r_script
78 if [ -e $pdf_report ] ; then
79 echo "Moving $xls_file to $XLS_OUT"
80 /bin/mv $pdf_report $PDF_OUT
81 else
82 echo ERROR failed to generate PDF report >&2
83 exit 1
84 fi
85 else
86 echo ERROR no R script to generate PDF report >&2
87 exit 1
88 fi
89 #
90 # Done