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comparison weeder2_wrapper.sh @ 0:496bc4eff47e draft

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Initial version.
author pjbriggs
date Wed, 19 Nov 2014 07:56:27 -0500
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children 3c5f10f7dd40
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-1:000000000000 0:496bc4eff47e
1 #!/bin/sh -e
2 #
3 # Wrapper script to run weeder2 as a Galaxy tool
4 #
5 # Usage: weeder_wrapper.sh FASTA_IN SPECIES_CODE MOTIFS_OUT MATRIX_OUT [ ARGS... ]
6 #
7 # ARGS: one or more arguments to supply directly to weeder2
8 #
9 # Process command line
10 FASTA_IN=$1
11 SPECIES_CODE=$2
12 MOTIFS_OUT=$3
13 MATRIX_OUT=$4
14 #
15 # Other arguments
16 ARGS=""
17 while [ ! -z "$5" ] ; do
18 ARGS="$ARGS $5"
19 shift
20 done
21 #
22 # Link to input file
23 ln -s $FASTA_IN
24 #
25 # Link to the FreqFiles directory as weeder2 executable
26 # expects it to be the same directory
27 freqfiles_dir=$WEEDER_FREQFILES_DIR
28 if [ -d $freqfiles_dir ] ; then
29 echo "Linking to FreqFiles directory"
30 ln -s $freqfiles_dir FreqFiles
31 else
32 echo "ERROR FreqFiles directory not found" >&2
33 exit 1
34 fi
35 #
36 # Construct names of input and output files
37 fasta=`basename $FASTA_IN`
38 motifs_out=$fasta.w2
39 matrix_out=$fasta.matrix.w2
40 #
41 # Construct and run weeder command
42 # NB weeder logs output to stderr so redirect to stdout
43 # to prevent the Galaxy tool reporting failure
44 weeder_cmd="weeder2 -f $fasta -O $SPECIES_CODE $ARGS"
45 echo "Running $weeder_cmd"
46 $weeder_cmd 2>&1
47 status=$?
48 if [ $status -ne 0 ] ; then
49 echo weeder2 command finished with nonzero exit code $status >&2
50 echo Command was: $weeder_cmd
51 exit $status
52 fi
53 #
54 # Move outputs to final destinations
55 if [ -e $motifs_out ] ; then
56 /bin/mv $motifs_out $MOTIFS_OUT
57 fi
58 if [ -e $matrix_out ] ; then
59 /bin/mv $matrix_out $MATRIX_OUT
60 fi
61 #
62 # Done