# HG changeset patch
# User timpalpant
# Date 1549738944 18000
# Node ID b43c420a6135bcc6983db8a5502a93b0c72e149f
# Parent  a77e126ae856eefe20dfacb9daefbee228abb74f
Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9

diff -r a77e126ae856 -r b43c420a6135 dist/java-genomics-toolkit.jar
Binary file dist/java-genomics-toolkit.jar has changed
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._Add.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._Autocorrelation.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._Average.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._BaseAlignCounts.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._Correlate.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._DNAPropertyCalculator.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._Divide.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._Downsample.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._DynaPro.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._FastqIlluminaToSanger.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._FindAbsoluteMaxima.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._FindBoundaryNucleosomes.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._FindNMers.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._FindOutlierRegions.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._GaussianSmooth.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._GeneTrackToBedGraph.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._GeneTrackToWig.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._GreedyCaller.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._InterpolateDiscontinuousData.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._IntervalAverager.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._IntervalLengthDistribution.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._IntervalStats.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._IntervalToBed.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._IntervalToWig.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._KMeans.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._LogTransform.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._MapDyads.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._MatrixAligner.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._MovingAverageSmooth.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._Multiply.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._PercusDecomposition.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._Phasogram.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._PowerSpectrum.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._ReadLengthDistributionMatrix.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._RollingReadLength.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._RomanNumeralize.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._Scale.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._Shift.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._StripMatrix.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._Subtract.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._Summary.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._ValueDistribution.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._WaveletTransform.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._ZScore.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._galaxyToolRunner.sh
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._log4j.properties
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/._matrix2png.xml
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diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/Add.xml
--- a/galaxy-conf/Add.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/Add.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigAdd" name="Add" version="1.1.0">
   <description>multiple (Big)Wig files</description>
-  <command interpreter="sh">
+  <command interpreter="bash">
     galaxyToolRunner.sh wigmath.Add -o $output
       #for $input in $inputs
         ${input.file}
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/Autocorrelation.xml
--- a/galaxy-conf/Autocorrelation.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/Autocorrelation.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="Autocovariance" name="Compute the autocovariance" version="2.0.0">
   <description>of data in a Wiggle file</description>
-  <command interpreter="sh">galaxyToolRunner.sh ngs.Autocorrelation -i $input -l $windows -m $max -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh ngs.Autocorrelation -i $input -l $windows -m $max -o $output</command>
   <inputs>
       <param format="bigwig,wig" name="input" type="data" label="Input data" />
       <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/Average.xml
--- a/galaxy-conf/Average.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/Average.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigAvg" name="Average" version="1.1.0">
   <description>multiple (Big)Wig files</description>
-  <command interpreter="sh">
+  <command interpreter="bash">
     galaxyToolRunner.sh wigmath.Average -o $output $file1 $file2
       #for $input in $inputs
         ${input.file}
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/BaseAlignCounts.xml
--- a/galaxy-conf/BaseAlignCounts.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/BaseAlignCounts.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="BaseAlignCounts" name="Calculate coverage" version="2.0.0">
   <description>of sequencing reads</description>
-  <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command>
   <inputs>
     <param name="input" type="data" format="sam,bam,bed,bedgraph" label="Sequencing reads" />
     <param name="X" type="integer" value="-1" label="In silico extension (-1 for fragment length)" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/Correlate.xml
--- a/galaxy-conf/Correlate.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/Correlate.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigCorrelate" name="Correlate" version="1.1.0">
   <description>multiple (Big)Wig files</description>
-  <command interpreter="sh">
+  <command interpreter="bash">
     galaxyToolRunner.sh wigmath.Correlate -w $window -s $step -t $type -o $output $file1 $file2
       #for $input in $inputs
         ${input.file}
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/DNAPropertyCalculator.xml
--- a/galaxy-conf/DNAPropertyCalculator.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/DNAPropertyCalculator.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="DNAPropertyCalculator" name="Calculate sequence-specific DNA properties" version="2.0.0">
   <description>for a genome</description>
-  <command interpreter="sh">galaxyToolRunner.sh dna.DNAPropertyCalculator -i 
+  <command interpreter="bash">galaxyToolRunner.sh dna.DNAPropertyCalculator -i 
     #if $refGenomeSource.genomeSource == "history":
       $refGenomeSource.ownFile
     #else
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/Divide.xml
--- a/galaxy-conf/Divide.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/Divide.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigDivide" name="Divide" version="1.1.0">
   <description>two (Big)Wig files</description>
-  <command interpreter="sh">galaxyToolRunner.sh wigmath.Divide -n $dividend -d $divisor -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh wigmath.Divide -n $dividend -d $divisor -o $output</command>
   <inputs>
     <param format="bigwig,wig" name="dividend" type="data" label="File 1 (dividend)" />
     <param format="bigwig,wig" name="divisor" type="data" label="File 2 (divisor)" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/Downsample.xml
--- a/galaxy-conf/Downsample.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/Downsample.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigDownsample" name="Downsample" version="1.1.0">
   <description>a (Big)Wig file</description>
-  <command interpreter="sh">galaxyToolRunner.sh wigmath.Downsample -i $input -m $metric -w $window -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh wigmath.Downsample -i $input -m $metric -w $window -o $output</command>
   <inputs>
       <param format="bigwig,wig" name="input" type="data" label="Original data" />
       <param name="window" type="integer" value="100" label="Window size (bp)" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/DynaPro.xml
--- a/galaxy-conf/DynaPro.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/DynaPro.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="DynaPro" name="Compute equilibrium nucleosome positions" version="1.1.0">
   <description>using DynaPro</description>
-  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.DynaPro -i $input -n $N 
+  <command interpreter="bash">galaxyToolRunner.sh nucleosomes.DynaPro -i $input -n $N 
     #if str( $mean ) != ''
       -m $mean 
     #end if
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/ExtractDataFromRegion.xml
--- a/galaxy-conf/ExtractDataFromRegion.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/ExtractDataFromRegion.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="ExtractDataFromWig" name="Extract data from a Wig file" version="1.0.0">
   <description>for a genomic interval</description>
-  <command interpreter="sh">
+  <command interpreter="bash">
   	galaxyToolRunner.sh ngs.ExtractDataFromRegion --chr $chr --start $start --stop $stop -o $output $file1
   	  #for $input in $inputs
         ${input.file}
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/FastqIlluminaToSanger.xml
--- a/galaxy-conf/FastqIlluminaToSanger.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/FastqIlluminaToSanger.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="FastqIlluminaToSanger" name="Convert Fastq qualities" version="1.0.0">
   <description>from Illumina to Sanger</description>
-  <command interpreter="sh">galaxyToolRunner.sh converters.FastqIlluminaToSanger -i $input -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh converters.FastqIlluminaToSanger -i $input -o $output</command>
   <inputs>
       <param name="input" type="data" format="fastqillumina" label="FASTQ, Illumina qualities" />
   </inputs>
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/FindAbsoluteMaxima.xml
--- a/galaxy-conf/FindAbsoluteMaxima.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/FindAbsoluteMaxima.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="FindWigMaxima" name="Find absolute maxima" version="1.1.0">
   <description>in intervals</description>
-  <command interpreter="sh">
+  <command interpreter="bash">
     galaxyToolRunner.sh ngs.FindAbsoluteMaxima -l $window -o $output
   	  #for $input in $inputs
         ${input.file}
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/FindBoundaryNucleosomes.xml
--- a/galaxy-conf/FindBoundaryNucleosomes.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/FindBoundaryNucleosomes.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="FindNuke" name="Find boundary nucleosomes" version="2.0.0">
   <description>in windows</description>
-  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.FindBoundaryNucleosomes -i $input -l $loci -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh nucleosomes.FindBoundaryNucleosomes -i $input -l $loci -o $output</command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Nucleosome calls" />
     <param name="loci" type="data" format="bed,bedgraph,gff" label="List of intervals" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/FindNMers.xml
--- a/galaxy-conf/FindNMers.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/FindNMers.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="FindNMers" name="Find NMers" version="1.0.0">
   <description>in a DNA sequence</description>
-  <command interpreter="sh">galaxyToolRunner.sh dna.FindNMers -i 
+  <command interpreter="bash">galaxyToolRunner.sh dna.FindNMers -i 
     #if $refGenomeSource.genomeSource == "history":
       $refGenomeSource.ownFile
     #else
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/FindOutlierRegions.xml
--- a/galaxy-conf/FindOutlierRegions.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/FindOutlierRegions.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigFindOutliers" name="Find outlier regions" version="1.1.0">
   <description>such as CNVs</description>
-  <command interpreter="sh">galaxyToolRunner.sh ngs.FindOutlierRegions -i $input -w $window -t $threshold $below -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh ngs.FindOutlierRegions -i $input -w $window -t $threshold $below -o $output</command>
   <inputs>
       <param format="bigwig,wig" name="input" type="data" label="Input data" />
       <param name="window" type="integer" value="150" label="Window size" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/GaussianSmooth.xml
--- a/galaxy-conf/GaussianSmooth.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/GaussianSmooth.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigGaussianSmooth" name="Gaussian smooth" version="1.1.0">
   <description>a (Big)Wig file</description>
-  <command interpreter="sh">galaxyToolRunner.sh wigmath.GaussianSmooth -i $input -s $S -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh wigmath.GaussianSmooth -i $input -s $S -o $output</command>
   <inputs>
       <param name="input" type="data" format="bigwig,wig" label="Smooth the data in" />
       <param name="S" type="integer" value="20" optional="true" label="Standard deviation of the Gaussian in base pairs" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/GeneTrackToBedGraph.xml
--- a/galaxy-conf/GeneTrackToBedGraph.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/GeneTrackToBedGraph.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="GeneTrackToBedGraph" name="GeneTrack to BedGraph" version="1.1.0">
   <description>converter</description>
-  <command interpreter="sh">galaxyToolRunner.sh converters.GeneTrackToBedGraph -i $input -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh converters.GeneTrackToBedGraph -i $input -o $output</command>
   <inputs>
       <param name="input" type="data" format="tabular" label="Input GeneTrack index" />
   </inputs>
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/GeneTrackToWig.xml
--- a/galaxy-conf/GeneTrackToWig.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/GeneTrackToWig.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="GeneTrackToWig" name="GeneTrack to Wig" version="1.1.0">
   <description>converter</description>
-  <command interpreter="sh">galaxyToolRunner.sh converters.GeneTrackToWig -i $input -s $shift $zero -a ${chromInfo} -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh converters.GeneTrackToWig -i $input -s $shift $zero -a ${chromInfo} -o $output</command>
   <inputs>
       <param name="input" type="data" format="tabular" label="Input GeneTrack index" />
       <param name="shift" type="integer" value="0" optional="true" label="Shift +/- strand counts by this amount when merging" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/GreedyCaller.xml
--- a/galaxy-conf/GreedyCaller.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/GreedyCaller.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="CallNukes" name="Call Nucleosomes" version="1.1.0">
   <description>in an MNase experiment</description>
-  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.GreedyCaller -d $dyads -s $smoothed -n $N -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh nucleosomes.GreedyCaller -d $dyads -s $smoothed -n $N -o $output</command>
   <inputs>
       <param name="dyads" type="data" format="bigwig,wig" label="Dyad counts" />
       <param name="smoothed" type="data" format="bigwig,wig" label="Smoothed dyad counts" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/InterpolateDiscontinuousData.xml
--- a/galaxy-conf/InterpolateDiscontinuousData.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/InterpolateDiscontinuousData.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigInterpolate" name="Interpolate" version="1.1.0">
   <description>missing values in a (Big)Wig file</description>
-  <command interpreter="sh">galaxyToolRunner.sh converters.InterpolateDiscontinousData -i $input -t $type -m $max -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh converters.InterpolateDiscontinousData -i $input -t $type -m $max -o $output</command>
   <inputs>
       <param format="bigwig,wig" name="input" type="data" label="Interpolate missing values in" />
       <param name="type" type="select" label="Interpolation type">
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/IntervalAverager.xml
--- a/galaxy-conf/IntervalAverager.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/IntervalAverager.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="IntervalAverager" name="Average intervals" version="2.1.0">
   <description>that have been aligned</description>
-  <command interpreter="sh">
+  <command interpreter="bash">
     galaxyToolRunner.sh visualization.IntervalAverager -l $loci -o $output $file1
       #for $input in $inputs
         ${input.file}
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/IntervalLengthDistribution.xml
--- a/galaxy-conf/IntervalLengthDistribution.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/IntervalLengthDistribution.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="IntervalLengthDistribution" name="Make histogram" version="1.0.0">
   <description>of read lengths</description>
-  <command interpreter="sh">galaxyToolRunner.sh ngs.IntervalLengthDistribution -i $input $freq -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh ngs.IntervalLengthDistribution -i $input $freq -o $output</command>
   <inputs>
       <param name="input" type="data" format="sam,bam,bed,bedgraph,gff" label="Reads/Intervals" />
       <param name="freq" type="boolean" checked="false" truevalue="-f" falsevalue="" label="Output normalized frequencies rather than counts" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/IntervalStats.xml
--- a/galaxy-conf/IntervalStats.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/IntervalStats.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="IntervalStats" name="Compute mean/min/max of intervals" version="1.0.0">
   <description>of data in a (Big)Wig file</description>
-  <command interpreter="sh">
+  <command interpreter="bash">
     galaxyToolRunner.sh ngs.IntervalStats -l $windows -s $stat -o $output
       #for $input in $inputs
         ${input.file}
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/IntervalToBed.xml
--- a/galaxy-conf/IntervalToBed.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/IntervalToBed.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="IntervalToBed" name="SAM/BAM/GFF/BedGraph/BigBed/VCF to Bed" version="1.0.0">
   <description>converter</description>
-  <command interpreter="sh">galaxyToolRunner.sh converters.IntervalToBed -i $input -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh converters.IntervalToBed -i $input -o $output</command>
   <inputs>
       <param name="input" type="data" format="sam,bam,gff,bigbed,bedgraph,vcf" label="Input" />
   </inputs>
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/IntervalToWig.xml
--- a/galaxy-conf/IntervalToWig.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/IntervalToWig.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="BedToWig" name="Bed/BedGraph/GFF to Wig" version="1.1.0">
   <description>converter</description>
-  <command interpreter="sh">galaxyToolRunner.sh converters.IntervalToWig -i $input $zero -a ${chromInfo} -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh converters.IntervalToWig -i $input $zero -a ${chromInfo} -o $output</command>
   <inputs>
       <param name="input" type="data" format="bed,bedgraph,gff" label="Input Bed/BedGraph/GFF file" />
   	  <param name="zero" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Assume zero where there is no data (default is NaN)" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/KMeans.xml
--- a/galaxy-conf/KMeans.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/KMeans.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="KMeans" name="KMeans cluster" version="1.0.0">
   <description>an aligned matrix</description>
-  <command interpreter="sh">galaxyToolRunner.sh visualization.KMeans -i $input -k $K -1 $min -2 $max -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh visualization.KMeans -i $input -k $K -1 $min -2 $max -o $output</command>
   <inputs>
     <param format="tabular" name="input" type="data" label="Aligned matrix" />
     <param name="K" type="integer" value="10" label="Number of clusters" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/LogTransform.xml
--- a/galaxy-conf/LogTransform.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/LogTransform.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigLogTransform" name="Log transform" version="1.1.0">
   <description>a (Big)Wig file</description>
-  <command interpreter="sh">galaxyToolRunner.sh wigmath.LogTransform -i $input -b $base -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh wigmath.LogTransform -i $input -b $base -o $output</command>
   <inputs>
     <param format="bigwig,wig" name="input" type="data" label="(Big)Wig file" />
     <param name="base" type="integer" value="2" label="Logarithm base" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/MapDyads.xml
--- a/galaxy-conf/MapDyads.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/MapDyads.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="MapDyads" name="Map dyads" version="1.1.0">
   <description>from sequencing reads</description>
-  <command interpreter="sh">
+  <command interpreter="bash">
     galaxyToolRunner.sh nucleosomes.MapDyads -i $input -a ${chromInfo} -o $output
     #if $type.read == 'single'
       -s $type.size
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/MatrixAligner.xml
--- a/galaxy-conf/MatrixAligner.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/MatrixAligner.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="MatrixAligner" name="Align values in a matrix" version="1.0.0">
   <description>for a heatmap</description>
-  <command interpreter="sh">galaxyToolRunner.sh visualization.MatrixAligner -i $input -l $loci -m $M -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh visualization.MatrixAligner -i $input -l $loci -m $M -o $output</command>
   <inputs>
       <param format="wig,bigwig" name="input" type="data" label="Sequencing data" />
       <param format="bed" name="loci" type="data" label="List of intervals (with alignment points)" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/MovingAverageSmooth.xml
--- a/galaxy-conf/MovingAverageSmooth.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/MovingAverageSmooth.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigMovingAverage" name="Moving average smooth" version="1.1.0">
   <description>a (Big)Wig file</description>
-  <command interpreter="sh">galaxyToolRunner.sh wigmath.MovingAverageSmooth -i $input -w $W -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh wigmath.MovingAverageSmooth -i $input -w $W -o $output</command>
   <inputs>
       <param name="input" type="data" format="bigwig,wig" label="Smooth the data in" />
       <param name="W" type="integer" value="20" optional="true" label="Width of the moving average in base pairs" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/Multiply.xml
--- a/galaxy-conf/Multiply.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/Multiply.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigMultiply" name="Multiply" version="1.1.0">
   <description>(Big)Wig files</description>
-  <command interpreter="sh">
+  <command interpreter="bash">
     galaxyToolRunner.sh wigmath.Multiply -o $output
       #for $input in $inputs
         ${input.file}
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/PairOverlappingNucleosomes.xml
--- a/galaxy-conf/PairOverlappingNucleosomes.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/PairOverlappingNucleosomes.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="PairNukes" name="Pair nucleosomes" version="1.0.0">
   <description>by overlap</description>
-  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.PairOverlappingNucleosomes -a $input1 -b $input2 -m $N -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh nucleosomes.PairOverlappingNucleosomes -a $input1 -b $input2 -m $N -o $output</command>
   <inputs>
       <param name="input1" type="data" format="tabular" label="Nucleosome calls 1" />
       <param name="input2" type="data" format="tabular" label="Nucleosome calls 2" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/PercusDecomposition.xml
--- a/galaxy-conf/PercusDecomposition.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/PercusDecomposition.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="PercusDecomposition" name="Derive Percus energy landscape" version="1.1.0">
   <description>from occupancy data</description>
-  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.PercusDecomposition -d $dyads -n $N -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh nucleosomes.PercusDecomposition -d $dyads -n $N -o $output</command>
   <inputs>
       <param name="dyads" type="data" format="bigwig,wig" label="Dyad counts (smoothed)" />
       <param name="N" type="integer" value="147" optional="true" label="Assumed nucleosome size" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/Phasogram.xml
--- a/galaxy-conf/Phasogram.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/Phasogram.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="Phasogram" name="Make phasogram" version="1.0.0">
   <description>of dyads</description>
-  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.Phasogram -i $input -m $max -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh nucleosomes.Phasogram -i $input -m $max -o $output</command>
   <inputs>
     <param name="input" type="data" format="bigwig,wig" label="Dyads (Big)Wig file" />
     <param name="max" type="integer" value="1000" label="Maximum phase shift (bp)" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/PowerSpectrum.xml
--- a/galaxy-conf/PowerSpectrum.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/PowerSpectrum.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="PowerSpectrum" name="Compute the power spectrum" version="1.0.0">
   <description>of data in a Wiggle file</description>
-  <command interpreter="sh">galaxyToolRunner.sh ngs.PowerSpectrum -i $input -l $windows -m $max -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh ngs.PowerSpectrum -i $input -l $windows -m $max -o $output</command>
   <inputs>
       <param format="bigwig,wig" name="input" type="data" label="Input data" />
       <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/ReadLengthDistributionMatrix.xml
--- a/galaxy-conf/ReadLengthDistributionMatrix.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/ReadLengthDistributionMatrix.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="ReadLengthDistributionMatrix" name="Create read length distribution matrix" version="1.0.0">
   <description>across a genomic interval</description>
-  <command interpreter="sh">galaxyToolRunner.sh ngs.ReadLengthDistributionMatrix -i $input --chr $chr --start $start --stop $stop --min $min --max $max --bin $bin -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh ngs.ReadLengthDistributionMatrix -i $input --chr $chr --start $start --stop $stop --min $min --max $max --bin $bin -o $output</command>
   <inputs>
       <param format="sam,bam,bed,bedgraph" name="input" type="data" label="Mapped reads" />
       <param name="chr" type="text" label="Chromosome" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/RollingReadLength.xml
--- a/galaxy-conf/RollingReadLength.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/RollingReadLength.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="RollingReadLength" name="Compute mean fragment length" version="1.1.0">
   <description>over each locus</description>
-  <command interpreter="sh">galaxyToolRunner.sh ngs.RollingReadLength -i $input -a ${chromInfo} -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh ngs.RollingReadLength -i $input -a ${chromInfo} -o $output</command>
   <inputs>
       <param format="sam,bam,bed,bedgraph" name="input" type="data" label="Mapped reads" />
   </inputs>
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/RomanNumeralize.xml
--- a/galaxy-conf/RomanNumeralize.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/RomanNumeralize.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="RomanNumeralize" name="Convert Arabic to Roman numerals" version="1.0.0">
   <description>on any file</description>
-  <command interpreter="sh">galaxyToolRunner.sh converters.RomanNumeralize -i $input -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh converters.RomanNumeralize -i $input -o $output</command>
   <inputs>
       <param name="input" type="data" label="Convert Arabic integer chromosome coordinates in" />
   </inputs>
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/Scale.xml
--- a/galaxy-conf/Scale.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/Scale.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigScale" name="Scale" version="1.2.0">
   <description>a (Big)Wig file</description>
-  <command interpreter="sh">galaxyToolRunner.sh wigmath.Scale -i $input -m $M $chr -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh wigmath.Scale -i $input -m $M $chr -o $output</command>
   <inputs>
     <param format="bigwig,wig" name="input" type="data" label="Scale the data in" />
     <param name="M" type="float" value="0" label="Multiply by (leave 0 to scale by 1/mean)" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/Shift.xml
--- a/galaxy-conf/Shift.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/Shift.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigShift" name="Mean shift" version="1.2.0">
   <description>a (Big)Wig file</description>
-  <command interpreter="sh">galaxyToolRunner.sh wigmath.Shift -i $input -m $M $chr -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh wigmath.Shift -i $input -m $M $chr -o $output</command>
   <inputs>
     <param format="bigwig,wig" name="input" type="data" label="Shift the data in" />
     <param name="M" type="float" value="0" label="To have mean" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/StripMatrix.xml
--- a/galaxy-conf/StripMatrix.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/StripMatrix.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="StripMatrix" name="Strip headers" version="1.1.0">
   <description>from an aligned matrix</description>
-  <command interpreter="sh">galaxyToolRunner.sh visualization.StripMatrix -i $input -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh visualization.StripMatrix -i $input -o $output</command>
   <inputs>
     <param format="tabular" name="input" type="data" label="Aligned matrix" />
   </inputs>
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/Subsample.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/Subsample.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -0,0 +1,16 @@
+<tool id="Subsample" name="Randomly select N entries" version="1.0.0">
+  <description>from an interval file</description>
+  <command interpreter="bash">galaxyToolRunner.sh ngs.Subsample -i $input -n $n -o $output</command>
+  <inputs>
+      <param name="input" type="data" format="sam,bam,gff,bed,bigbed,bedgraph,vcf" label="Input file" />
+  </inputs>
+  <outputs>
+      <data name="output" format="input" metadata_source="input" />
+  </outputs>
+  
+<help>
+  
+This tool will randomly select N reads from a file.
+
+</help>
+</tool>
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/Subtract.xml
--- a/galaxy-conf/Subtract.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/Subtract.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigSubtract" name="Subtract" version="1.1.0">
   <description>two (Big)Wig files</description>
-  <command interpreter="sh">galaxyToolRunner.sh wigmath.Subtract -m $minuend -s $subtrahend -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh wigmath.Subtract -m $minuend -s $subtrahend -o $output</command>
   <inputs>
     <param format="bigwig,wig" name="minuend" type="data" label="File 1 (minuend / top)" />
     <param format="bigwig,wig" name="subtrahend" type="data" label="File 2 (subtrahend / bottom)" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/Summary.xml
--- a/galaxy-conf/Summary.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/Summary.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigSummary" name="Output a summary" version="1.1.0">
   <description>of a (Big)Wig file</description>
-  <command interpreter="sh">galaxyToolRunner.sh wigmath.Summary -i $input -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh wigmath.Summary -i $input -o $output</command>
   <inputs>
       <param format="bigwig,wig" name="input" type="data" label="(Big)Wig file" />
   </inputs>
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/ValueDistribution.xml
--- a/galaxy-conf/ValueDistribution.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/ValueDistribution.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigValueDistribution" name="Compute the value distribution" version="1.1.0">
   <description>of a (Big)Wig file</description>
-  <command interpreter="sh">galaxyToolRunner.sh wigmath.ValueDistribution -i $input 
+  <command interpreter="bash">galaxyToolRunner.sh wigmath.ValueDistribution -i $input 
     #if str( $min ) != ''
       --min $min
     #end if
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/WaveletTransform.xml
--- a/galaxy-conf/WaveletTransform.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/WaveletTransform.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WaveletTransform" name="Wavelet analysis" version="1.0.0">
   <description>across a genomic interval</description>
-  <command interpreter="sh">galaxyToolRunner.sh ngs.WaveletTransform -i $input -w $wavelet --chr $chr --start $start --stop $stop --min $min --max $max --step $N -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh ngs.WaveletTransform -i $input -w $wavelet --chr $chr --start $start --stop $stop --min $min --max $max --step $N -o $output</command>
   <inputs>
       <param format="wig,bigwig" name="input" type="data" label="Sequencing data" />
       <param format="tabular" name="wavelet" type="data" label="Wavelet" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/ZScore.xml
--- a/galaxy-conf/ZScore.xml	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/ZScore.xml	Sat Feb 09 14:02:24 2019 -0500
@@ -1,6 +1,6 @@
 <tool id="WigZScore" name="Z-Score" version="1.2.0">
   <description>a (Big)Wig file</description>
-  <command interpreter="sh">galaxyToolRunner.sh wigmath.ZScore -i $input $chr -o $output</command>
+  <command interpreter="bash">galaxyToolRunner.sh wigmath.ZScore -i $input $chr -o $output</command>
   <inputs>
       <param format="bigwig,wig" name="input" type="data" label="Z-score the data in" />
       <param name="chr" type="boolean" checked="false" truevalue="--bychr" falsevalue="" label="Z-score chromosomes individually" />
diff -r a77e126ae856 -r b43c420a6135 galaxy-conf/galaxyToolRunner.sh
--- a/galaxy-conf/galaxyToolRunner.sh	Tue Jun 19 22:15:09 2012 -0400
+++ b/galaxy-conf/galaxyToolRunner.sh	Sat Feb 09 14:02:24 2019 -0500
@@ -6,13 +6,5 @@
   exit;
 fi
 
-# Verify that the user has Java 7 installed
-# Otherwise there will be an obscure UnsupportedClassVersion error
-version=$(java -version 2>&1 | awk -F '"' '/version/ {print $2}')
-if [[ "$version" < "1.7" ]]; then
-    echo "Need Java 7 or greater. You have Java $version installed."
-    exit
-fi
-
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-java -Dlog4j.configuration=log4j.properties -cp $DIR:$DIR/../build:$DIR/../dist/*:$DIR/../lib/* edu.unc.genomics."$@"
\ No newline at end of file
+java -Dlog4j.configuration=log4j.properties -cp $DIR:$DIR/../build:$DIR/../dist/*:$DIR/../lib/* edu.unc.genomics."$@"
diff -r a77e126ae856 -r b43c420a6135 lib/JLargeArrays-1.2.jar
Binary file lib/JLargeArrays-1.2.jar has changed
diff -r a77e126ae856 -r b43c420a6135 lib/JTransforms-3.0.jar
Binary file lib/JTransforms-3.0.jar has changed
diff -r a77e126ae856 -r b43c420a6135 lib/java-genomics-io.jar
Binary file lib/java-genomics-io.jar has changed
diff -r a77e126ae856 -r b43c420a6135 lib/jtransforms-2.4.jar
Binary file lib/jtransforms-2.4.jar has changed