Mercurial > repos > pjbriggs > weeder2
view weeder2_wrapper.sh @ 3:f19e18ab01b1 draft
Uploaded v2.0.2 (use conda for dependency resolution)
author | pjbriggs |
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date | Mon, 05 Mar 2018 10:19:50 -0500 |
parents | 3c5f10f7dd40 |
children | 89315bdc1a8c |
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#!/bin/sh -e # # Wrapper script to run weeder2 as a Galaxy tool # # Usage: weeder_wrapper.sh FASTA_IN SPECIES_CODE FREQFILES_DIR MOTIFS_OUT MATRIX_OUT [ ARGS... ] # # ARGS: one or more arguments to supply directly to weeder2 # # Process command line FASTA_IN=$1 SPECIES_CODE=$2 FREQFILES_DIR=$3 MOTIFS_OUT=$4 MATRIX_OUT=$5 # # Other arguments ARGS="" while [ ! -z "$6" ] ; do ARGS="$ARGS $6" shift done # # Link to input file ln -s $FASTA_IN # # Locate the FreqFiles directory if [ $FREQFILES_DIR == "." ] ; then # Use the files in the Weeder2 distribution freqfiles_dir=$WEEDER_FREQFILES_DIR else # Alternative location freqfiles_dir=$FREQFILES_DIR fi # # Link to the FreqFiles directory as weeder2 executable # expects it to be the same directory if [ -d $freqfiles_dir ] ; then echo "Linking to FreqFiles directory: $freqfiles_dir" ln -s $freqfiles_dir FreqFiles else echo "ERROR FreqFiles directory not found" >&2 exit 1 fi # # Construct names of input and output files fasta=`basename $FASTA_IN` motifs_out=$fasta.w2 matrix_out=$fasta.matrix.w2 # # Construct and run weeder command # NB weeder logs output to stderr so redirect to stdout # to prevent the Galaxy tool reporting failure weeder_cmd="weeder2 -f $fasta -O $SPECIES_CODE $ARGS" echo "Running $weeder_cmd" $weeder_cmd 2>&1 status=$? if [ $status -ne 0 ] ; then echo weeder2 command finished with nonzero exit code $status >&2 echo Command was: $weeder_cmd exit $status fi # # Move outputs to final destinations if [ -e $motifs_out ] ; then /bin/mv $motifs_out $MOTIFS_OUT fi if [ -e $matrix_out ] ; then /bin/mv $matrix_out $MATRIX_OUT fi # # Done