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comparison ceas_wrapper.sh @ 4:4e2883bb058d draft

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Synchronise version with one on main toolshed (version of 30/06/2015)
author pjbriggs
date Wed, 10 Aug 2016 11:04:42 -0400
parents 82df5af2995f
children
comparison
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3:82df5af2995f 4:4e2883bb058d
4 # 4 #
5 # This runs the Cistrome versions of CEAS, which provides two executables: 5 # This runs the Cistrome versions of CEAS, which provides two executables:
6 # - ceas (same as the "official" version) 6 # - ceas (same as the "official" version)
7 # - ceasBW (modified version that accepts a bigwig file as input) 7 # - ceasBW (modified version that accepts a bigwig file as input)
8 # 8 #
9 # Usage: ceas_wrapper.sh $BED_IN $GDB_IN $EXTRA_BED_IN $LOG_OUT $PDF_OUT $XLS_OUT $DBKEY 9 # Usage: ceas_wrapper.sh $BED_IN $GDB_IN $LOG_OUT $PDF_OUT $XLS_OUT [OPTIONS]
10 #
11 # Initialise
12 CEAS=ceas
10 # 13 #
11 # Process command line 14 # Process command line
12 echo $* 15 echo $*
13 BED_IN=$1 16 BED_IN=$1
14 GDB_IN=$2 17 GDB_IN=$2
15 EXTRA_BED_IN=$3 18 LOG_OUT=$3
16 LOG_OUT=$4 19 PDF_OUT=$4
17 PDF_OUT=$5 20 XLS_OUT=$5
18 XLS_OUT=$6 21 #
22 # Initialise other variables
23 EXTRA_BED_IN=
19 # 24 #
20 # Collect remaining args 25 # Collect remaining args
21 CEAS=ceas
22 OPTIONS= 26 OPTIONS=
23 while [ ! -z "$7" ] ; do 27 while [ ! -z "$6" ] ; do
24 if [ "$7" == "--bigwig" ] ; then 28 if [ "$6" == "--bigwig" ] ; then
29 # Bigwig input, need to use 'ceasBW'
25 CEAS=ceasBW 30 CEAS=ceasBW
31 OPTIONS="$OPTIONS --bigwig"
32 elif [ "$6" == "--length" ] ; then
33 # Need a chrom sizes file
34 chrom_sizes=$7
35 if [ ! -f "$chrom_sizes" ] ; then
36 # If chrom sizes file doesn't already exist then attempt to
37 # download the data from UCSC
38 echo "WARNING no file $chrom_sizes"
39 dbkey=$(echo $(basename $chrom_sizes) | cut -d'.' -f1)
40 if [ $dbkey == '?' ] ; then
41 # DBkey not set, this is fatal
42 echo "ERROR genome build not set, cannot get sizes for '?'" >&2
43 echo "Assign a genome build to your input dataset and rerun" >&2
44 exit 1
45 fi
46 # Fetch the sizes using fetchChromSizes
47 echo -n "Attempting to download chromosome sizes for $dbkey..."
48 chrom_sizes=$(basename $chrom_sizes)
49 fetchChromSizes $dbkey >$chrom_sizes 2>/dev/null
50 if [ $? -ne 0 ] ; then
51 echo "failed"
52 echo "ERROR unable to fetch data for ${dbkey}" >&2
53 echo "Please check the genome build associated with your input dataset" >&2
54 echo "or update your Galaxy instance to include an appropriate .len file" >&2
55 exit 1
56 else
57 echo "ok"
58 fi
59 fi
60 OPTIONS="$OPTIONS --length $chrom_sizes"
61 shift
62 else
63 OPTIONS="$OPTIONS $6"
26 fi 64 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 $7"
36 shift 65 shift
37 done 66 done
38 # 67 #
39 # Convenience variables for local files 68 # Convenience variables for local files
40 base_name="ceas" 69 base_name="ceas"
41 log_file=${base_name}.log 70 log_file=${base_name}.log
42 r_script=${base_name}.R
43 pdf_report=${base_name}.pdf 71 pdf_report=${base_name}.pdf
44 xls_file=${base_name}.xls 72 xls_file=${base_name}.xls
45 # 73 #
46 # Get CEAS version 74 # Get CEAS version
47 echo Running $CEAS 75 echo Running $CEAS
48 $CEAS --version >$log_file 2>/dev/null 76 $CEAS --version >$log_file 2>/dev/null
49 # 77 #
50 # Construct and run CEAS command line 78 # Construct and run CEAS command line
51 ceas_cmd="$CEAS --name $base_name $OPTIONS -g $GDB_IN -b $BED_IN" 79 ceas_cmd="$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" 80 echo "Running $ceas_cmd"
56 $ceas_cmd >>$log_file 2>&1 81 $ceas_cmd >>$log_file 2>&1
82 status=$?
83 if [ $status -ne 0 ] ; then
84 echo "Error: log file tail:"
85 tail $log_file
86 echo "ERROR $CEAS exited with non-zero code: $status" >&2
87 exit $status
88 fi
57 # 89 #
58 # Move outputs to final destination 90 # Move outputs to final destination
59 if [ -e $log_file ] ; then 91 if [ -e $log_file ] ; then
60 echo "Moving $log_file to $LOG_OUT" 92 echo "Moving $log_file to $LOG_OUT"
61 /bin/mv $log_file $LOG_OUT 93 /bin/mv $log_file $LOG_OUT
68 /bin/mv $xls_file $XLS_OUT 100 /bin/mv $xls_file $XLS_OUT
69 else 101 else
70 echo ERROR failed to generate XLS file >&2 102 echo ERROR failed to generate XLS file >&2
71 exit 1 103 exit 1
72 fi 104 fi
73 # 105 if [ -e $pdf_report ] ; then
74 # Run the R script to generate the PDF report 106 echo "Moving $pdf_report to $PDF_OUT"
75 if [ -e $r_script ] ; then 107 /bin/mv $pdf_report $PDF_OUT
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 108 else
86 echo ERROR no R script to generate PDF report >&2 109 echo ERROR failed to generate PDF report >&2
87 exit 1 110 exit 1
88 fi 111 fi
89 # 112 #
90 # Done 113 # Done