ceas: ceas_wrapper.sh annotate

annotate ceas_wrapper.sh @ 3:82df5af2995f draft

Renamed from "ceasbw..." to "ceas...".

author	pjbriggs
date	Wed, 22 Apr 2015 05:34:06 -0400
parents
children	4e2883bb058d

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

Mercurial > repos > pjbriggs > ceas

annotate ceas_wrapper.sh @ 3:82df5af2995f draft