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comparison ceasbw_wrapper.sh @ 0:8b25779ee261 draft

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Uploaded initial version to test toolshed.
author pjbriggs
date Wed, 28 Jan 2015 04:50:01 -0500
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children 695d61decd06
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-1:000000000000 0:8b25779ee261
1 #!/bin/sh -e
2 #
3 # Wrapper script to run CEASbw as a Galaxy tool
4 #
5 # Usage: ceasbw_wrapper.sh $BED_IN $GDB_IN $EXTRA_BED_IN $LOG_OUT $PDF_OUT $XLS_OUT $DBKEY
6 #
7 # Process command line
8 echo $*
9 BED_IN=$1
10 GDB_IN=$2
11 EXTRA_BED_IN=$3
12 LOG_OUT=$4
13 PDF_OUT=$5
14 XLS_OUT=$6
15 #
16 # Collect remaining args
17 CEAS=ceas
18 OPTIONS=
19 while [ ! -z "$7" ] ; do
20 if [ "$7" == "--bigwig" ] ; then
21 CEAS=ceasBW
22 fi
23 OPTIONS="$OPTIONS $7"
24 shift
25 done
26 #
27 # Convenience variables for local files
28 base_name="ceas"
29 log_file=${base_name}.log
30 r_script=${base_name}.R
31 pdf_report=${base_name}.pdf
32 xls_file=${base_name}.xls
33 #
34 # Get CEAS version
35 echo Running $CEAS
36 $CEAS --version >$log_file 2>/dev/null
37 #
38 # Construct and run CEAS command line
39 ceas_cmd="$CEAS --name $base_name $OPTIONS -g $GDB_IN -b $BED_IN"
40 if [ "$EXTRA_BED_IN" != "None" ] ; then
41 ceas_cmd="$ceas_cmd -e $EXTRA_BED_IN"
42 fi
43 echo "Running $ceas_cmd"
44 $ceas_cmd >>$log_file 2>&1
45 #
46 # Move outputs to final destination
47 if [ -e $log_file ] ; then
48 echo "Moving $log_file to $LOG_OUT"
49 /bin/mv $log_file $LOG_OUT
50 else
51 echo ERROR failed to make log file >&2
52 exit 1
53 fi
54 if [ -e $xls_file ] ; then
55 echo "Moving $xls_file to $XLS_OUT"
56 /bin/mv $xls_file $XLS_OUT
57 else
58 echo ERROR failed to generate XLS file >&2
59 exit 1
60 fi
61 #
62 # Run the R script to generate the PDF report
63 if [ -e $r_script ] ; then
64 echo "Running $r_script to generate $pdf_report"
65 R --vanilla < $r_script
66 if [ -e $pdf_report ] ; then
67 echo "Moving $xls_file to $XLS_OUT"
68 /bin/mv $pdf_report $PDF_OUT
69 else
70 echo ERROR failed to generate PDF report >&2
71 exit 1
72 fi
73 else
74 echo ERROR no R script to generate PDF report >&2
75 exit 1
76 fi
77 #
78 # Done