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comparison weeder2_wrapper.sh @ 0:fb7e680232af draft

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Uploaded v2.0.2
author pjbriggs
date Mon, 05 Mar 2018 06:21:11 -0500
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children 79f075dc6cfb
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-1:000000000000 0:fb7e680232af
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 FREQFILES_DIR 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 FREQFILES_DIR=$3
13 MOTIFS_OUT=$4
14 MATRIX_OUT=$5
15 #
16 # Other arguments
17 ARGS=""
18 while [ ! -z "$6" ] ; do
19 ARGS="$ARGS $6"
20 shift
21 done
22 #
23 # Link to input file
24 ln -s $FASTA_IN
25 #
26 # Locate the FreqFiles directory
27 if [ $FREQFILES_DIR == "." ] ; then
28 # Use the files in the Weeder2 distribution
29 freqfiles_dir=$WEEDER_FREQFILES_DIR
30 else
31 # Alternative location
32 freqfiles_dir=$FREQFILES_DIR
33 fi
34 #
35 # Link to the FreqFiles directory as weeder2 executable
36 # expects it to be the same directory
37 if [ -d $freqfiles_dir ] ; then
38 echo "Linking to FreqFiles directory: $freqfiles_dir"
39 ln -s $freqfiles_dir FreqFiles
40 else
41 echo "ERROR FreqFiles directory not found" >&2
42 exit 1
43 fi
44 #
45 # Construct names of input and output files
46 fasta=`basename $FASTA_IN`
47 motifs_out=$fasta.w2
48 matrix_out=$fasta.matrix.w2
49 #
50 # Construct and run weeder command
51 # NB weeder logs output to stderr so redirect to stdout
52 # to prevent the Galaxy tool reporting failure
53 weeder_cmd="weeder2 -f $fasta -O $SPECIES_CODE $ARGS"
54 echo "Running $weeder_cmd"
55 $weeder_cmd 2>&1
56 status=$?
57 if [ $status -ne 0 ] ; then
58 echo weeder2 command finished with nonzero exit code $status >&2
59 echo Command was: $weeder_cmd
60 exit $status
61 fi
62 #
63 # Move outputs to final destinations
64 if [ -e $motifs_out ] ; then
65 /bin/mv $motifs_out $MOTIFS_OUT
66 fi
67 if [ -e $matrix_out ] ; then
68 /bin/mv $matrix_out $MATRIX_OUT
69 fi
70 #
71 # Done