ceas: ceas_wrapper.sh annotate

annotate ceas_wrapper.sh @ 11:d3bd9caee1b7 draft default tip

Uploaded version 1.0.2-4.

author	pjbriggs
date	Wed, 26 Sep 2018 06:37:20 -0400
parents	4e2883bb058d
children

rev	line source
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	1 #!/bin/sh -e
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	2 #
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	3 # Wrapper script to run CEAS as a Galaxy tool
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	4 #
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	5 # This runs the Cistrome versions of CEAS, which provides two executables:
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	6 # - ceas (same as the "official" version)
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	7 # - ceasBW (modified version that accepts a bigwig file as input)
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	8 #
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	9 # Usage: ceas_wrapper.sh $BED_IN $GDB_IN $LOG_OUT $PDF_OUT $XLS_OUT [OPTIONS]
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	10 #
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	11 # Initialise
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	12 CEAS=ceas
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	13 #
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	14 # Process command line
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	15 echo $*
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	16 BED_IN=$1
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	17 GDB_IN=$2
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	18 LOG_OUT=$3
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	19 PDF_OUT=$4
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	20 XLS_OUT=$5
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	21 #
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	22 # Initialise other variables
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	23 EXTRA_BED_IN=
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	24 #
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	25 # Collect remaining args
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	26 OPTIONS=
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	27 while [ ! -z "$6" ] ; do
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	28 if [ "$6" == "--bigwig" ] ; then
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	29 # Bigwig input, need to use 'ceasBW'
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	30 CEAS=ceasBW
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	31 OPTIONS="$OPTIONS --bigwig"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	32 elif [ "$6" == "--length" ] ; then
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	33 # Need a chrom sizes file
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	34 chrom_sizes=$7
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	35 if [ ! -f "$chrom_sizes" ] ; then
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	36 # If chrom sizes file doesn't already exist then attempt to
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	37 # download the data from UCSC
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	38 echo "WARNING no file $chrom_sizes"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	39 dbkey=$(echo $(basename $chrom_sizes) \| cut -d'.' -f1)
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	40 if [ $dbkey == '?' ] ; then
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	41 # DBkey not set, this is fatal
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	42 echo "ERROR genome build not set, cannot get sizes for '?'" >&2
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	43 echo "Assign a genome build to your input dataset and rerun" >&2
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	44 exit 1
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	45 fi
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	46 # Fetch the sizes using fetchChromSizes
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	47 echo -n "Attempting to download chromosome sizes for $dbkey..."
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	48 chrom_sizes=$(basename $chrom_sizes)
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	49 fetchChromSizes $dbkey >$chrom_sizes 2>/dev/null
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	50 if [ $? -ne 0 ] ; then
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	51 echo "failed"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	52 echo "ERROR unable to fetch data for ${dbkey}" >&2
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	53 echo "Please check the genome build associated with your input dataset" >&2
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	54 echo "or update your Galaxy instance to include an appropriate .len file" >&2
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	55 exit 1
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	56 else
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	57 echo "ok"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	58 fi
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	59 fi
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	60 OPTIONS="$OPTIONS --length $chrom_sizes"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	61 shift
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	62 else
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	63 OPTIONS="$OPTIONS $6"
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	64 fi
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	65 shift
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	66 done
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	67 #
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	68 # Convenience variables for local files
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	69 base_name="ceas"
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	70 log_file=${base_name}.log
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	71 pdf_report=${base_name}.pdf
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	72 xls_file=${base_name}.xls
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	73 #
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	74 # Get CEAS version
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	75 echo Running $CEAS
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	76 $CEAS --version >$log_file 2>/dev/null
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	77 #
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	78 # Construct and run CEAS command line
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	79 ceas_cmd="$CEAS --name $base_name $OPTIONS -g $GDB_IN -b $BED_IN"
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	80 echo "Running $ceas_cmd"
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	81 $ceas_cmd >>$log_file 2>&1
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	82 status=$?
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	83 if [ $status -ne 0 ] ; then
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	84 echo "Error: log file tail:"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	85 tail $log_file
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	86 echo "ERROR $CEAS exited with non-zero code: $status" >&2
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	87 exit $status
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	88 fi
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	89 #
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	90 # Move outputs to final destination
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	91 if [ -e $log_file ] ; then
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	92 echo "Moving $log_file to $LOG_OUT"
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	93 /bin/mv $log_file $LOG_OUT
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	94 else
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	95 echo ERROR failed to make log file >&2
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	96 exit 1
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	97 fi
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	98 if [ -e $xls_file ] ; then
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	99 echo "Moving $xls_file to $XLS_OUT"
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	100 /bin/mv $xls_file $XLS_OUT
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	101 else
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	102 echo ERROR failed to generate XLS file >&2
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	103 exit 1
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	104 fi
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	105 if [ -e $pdf_report ] ; then
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	106 echo "Moving $pdf_report to $PDF_OUT"
4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	107 /bin/mv $pdf_report $PDF_OUT
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	108 else
4 4e2883bb058d Synchronise version with one on main toolshed (version of 30/06/2015) pjbriggs parents: 3 diff changeset	109 echo ERROR failed to generate PDF report >&2
3 82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	110 exit 1
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	111 fi
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	112 #
82df5af2995f Renamed from "ceasbw..." to "ceas...". pjbriggs parents: diff changeset	113 # Done

Mercurial > repos > pjbriggs > ceas

annotate ceas_wrapper.sh @ 11:d3bd9caee1b7 draft default tip