Mercurial > repos > pjbriggs > weeder2

comparison weeder2_wrapper.sh @ 4:89315bdc1a8c draft default tip

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Uploaded tool version 2.0.3.
author pjbriggs
date Wed, 26 Sep 2018 10:12:56 -0400
parents 3c5f10f7dd40
children
comparison
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3:f19e18ab01b1 4:89315bdc1a8c
23 # Link to input file 23 # Link to input file
24 ln -s $FASTA_IN 24 ln -s $FASTA_IN
25 # 25 #
26 # Locate the FreqFiles directory 26 # Locate the FreqFiles directory
27 if [ $FREQFILES_DIR == "." ] ; then 27 if [ $FREQFILES_DIR == "." ] ; then
28 # Use the files in the Weeder2 distribution 28 # Don't explicitly set the location - Weeder2 from
29 freqfiles_dir=$WEEDER_FREQFILES_DIR 29 # bioconda handles this automatically
30 freqfiles_dir=
30 else 31 else
31 # Alternative location 32 # Alternative location
32 freqfiles_dir=$FREQFILES_DIR 33 freqfiles_dir=$FREQFILES_DIR
33 fi 34 fi
34 # 35 #
35 # Link to the FreqFiles directory as weeder2 executable 36 # Link to the FreqFiles directory as weeder2 executable
36 # expects it to be the same directory 37 # expects it to be the same directory
37 if [ -d $freqfiles_dir ] ; then 38 if [ ! -z "$freqfiles_dir" ] ; then
38 echo "Linking to FreqFiles directory: $freqfiles_dir" 39 if [ -d $freqfiles_dir ] ; then
39 ln -s $freqfiles_dir FreqFiles 40 echo "Linking to FreqFiles directory: $freqfiles_dir"
41 ln -s $freqfiles_dir FreqFiles
42 else
43 echo "ERROR FreqFiles directory not found" >&2
44 exit 1
45 fi
40 else 46 else
41 echo "ERROR FreqFiles directory not found" >&2 47 echo "WARNING FreqFiles directory not set" >&2
42 exit 1
43 fi 48 fi
44 # 49 #
45 # Construct names of input and output files 50 # Construct names of input and output files
46 fasta=`basename $FASTA_IN` 51 fasta=$(basename $FASTA_IN)
47 motifs_out=$fasta.w2 52 motifs_out=${fasta}.w2
48 matrix_out=$fasta.matrix.w2 53 matrix_out=${fasta}.matrix.w2
49 # 54 #
50 # Construct and run weeder command 55 # Construct and run weeder command
51 # NB weeder logs output to stderr so redirect to stdout 56 # NB weeder logs output to stderr so redirect to stdout
52 # to prevent the Galaxy tool reporting failure 57 # to prevent the Galaxy tool reporting failure
53 weeder_cmd="weeder2 -f $fasta -O $SPECIES_CODE $ARGS" 58 weeder_cmd="weeder2 -f $fasta -O $SPECIES_CODE $ARGS"
61 fi 66 fi
62 # 67 #
63 # Move outputs to final destinations 68 # Move outputs to final destinations
64 if [ -e $motifs_out ] ; then 69 if [ -e $motifs_out ] ; then
65 /bin/mv $motifs_out $MOTIFS_OUT 70 /bin/mv $motifs_out $MOTIFS_OUT
71 else
72 echo ERROR missing output file: $motifs_out >&2
73 status=1
66 fi 74 fi
67 if [ -e $matrix_out ] ; then 75 if [ -e $matrix_out ] ; then
68 /bin/mv $matrix_out $MATRIX_OUT 76 /bin/mv $matrix_out $MATRIX_OUT
77 else
78 echo ERROR missing output file: $matrix_out >&2
79 status=1
69 fi 80 fi
70 # 81 #
71 # Done 82 # Done
83 exit $status