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changeset 8:ad32956798e3 draft

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Uploaded
author nikos
date Tue, 02 Sep 2014 12:04:30 -0400
parents eebdd6da9353
children c3bbf6737487
files bedClip.sh bedClip.xml bedExtendRanges.xml bigWigSummary.xml bigwig2summary.sh bigwig2summary.xml test-data/1.bed test-data/1.bigwig test-data/1.tabular test-data/1.txt test-data/2.bed test-data/2.tabular test-data/3.bed test-data/4.bed tool_dependencies.xml
diffstat 15 files changed, 530 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bedClip.sh	Tue Sep 02 12:04:30 2014 -0400
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+bedClip $1 <(fetchChromSizes $2 2> /dev/null) $3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bedClip.xml	Tue Sep 02 12:04:30 2014 -0400
@@ -0,0 +1,65 @@
+<tool id="bedClip" name="bedClip">
+    <description> Remove lines from bed file that refer to off-chromosome places.</description>
+    <requirements>
+        <requirement type="package" version="1.0">fetchChromSizes</requirement>
+        <requirement type="package" version="1.0">bedClip</requirement>
+    </requirements>
+    <command interpreter="bash"> 
+	## Set genome assembly 
+
+	#set $Genome = str( $genome_cond.genome )
+	#if str( $genome_cond ) == 'OTHER':
+		#set $Genome = str( $genome_cond.genome_other )
+	#end if
+	
+	bedClip.sh $input $Genome $output
+    </command>
+    <inputs>
+        <param name="input" type="data" format="bed" label="Input"/>
+        <conditional name="genome_cond">
+	    <param name="genome" type="select" label="Genome Assembly">
+        	<option value="hg19">Human (Homo sapiens): hg19</option>
+	        <option value="hg18">Human (Homo sapiens): hg18</option>
+        	<option value="mm10">Mouse (Mus musculus): mm10</option>
+	        <option value="mm9">Mouse (Mus musculus): mm9</option>
+        	<option value="ce10">C. elegans: ce10</option>
+	        <option value="ce6">C. elegans: ce6</option>
+        	<option value="dm3">D. melanogaster: dm3</option>
+	        <option value="OTHER">Other</option>
+            </param>
+	    <when value="OTHER">
+        	<param name="genome_other" type="text" label="Other genome assemly"/>
+      	    </when>
+	    <when value="hg19" type="text" />
+      	    <when value="hg18" type="text" />
+      	    <when value="mm10" type="text" />
+      	    <when value="mm9" type="text" />
+	    <when value="ce10" type="text" />
+	    <when value="ce6" type="text" />
+	    <when value="dm3" type="text" />
+	</conditional>
+
+    </inputs>
+  
+    <outputs>
+        <data format="input" name="output"/> 
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="input" value="3.bed" />
+            <param name="genome" value="hg19" />
+            <output name="output" file="1.bed" />
+        </test>
+    </tests>
+
+    <help>
+**What it does**
+bedClip - Remove lines from bed file that refer to off-chromosome places.
+
+**Usage**
+
+  bedClip input.bed chrom.sizes output.bed
+
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bedExtendRanges.xml	Tue Sep 02 12:04:30 2014 -0400
@@ -0,0 +1,82 @@
+<tool id="bedExtendRanges" name="bedExtendRanges">
+    <description> Extend length of entries in bed 6+. </description>
+    <requirements>
+        <requirement type="package" version="1.0">bedExtendRanges</requirement>
+    </requirements>
+    <command> 
+	## Set genome assembly 
+
+	#set $Genome = str( $genome_cond.genome )
+	#if str( $genome_cond ) == 'OTHER':
+		#set $Genome = str( $genome_cond.genome_other )
+	#end if
+	
+	bedExtendRanges -user=genome -host=genome-mysql.cse.ucsc.edu $Genome $length $input 2> /dev/null > $output
+    </command>
+    <inputs>
+        <param name="input" type="data" format="bed" label="Input"/>
+        <conditional name="genome_cond">
+            <param name="genome" type="select" label="Genome Assembly (-g)">
+	        <option value="hg19">Human (Homo sapiens): hg19</option>
+        	<option value="hg18">Human (Homo sapiens): hg18</option>
+	        <option value="mm10">Mouse (Mus musculus): mm10</option>
+        	<option value="mm9">Mouse (Mus musculus): mm9</option>
+        	<option value="ce10">C. elegans: ce10</option>
+	        <option value="ce6">C. elegans: ce6</option>
+	        <option value="dm3">D. melanogaster: dm3</option>
+        	<option value="OTHER">Other</option>
+            </param>
+            <when value="OTHER">
+      		<param name="genome_other" type="text" label="Other genome assemly"/>
+            </when>
+      	    <when value="hg19" type="text" />
+            <when value="hg18" type="text" />
+      	    <when value="mm10" type="text" />
+            <when value="mm9" type="text" />
+            <when value="ce10" type="text" />
+            <when value="ce6" type="text" />
+            <when value="dm3" type="text" />
+    	</conditional>
+        <param name="length" type="integer" value="0" label="Length extension (base-pairs)" />
+
+    </inputs>
+  
+    <outputs>
+        <data format="input" name="output"/> 
+    </outputs>
+
+    <tests>
+	<test>
+	    <param name="input" value="2.bed" />
+	    <param name="genome" value="hg19" />
+	    <param name="length" value="5000" />
+	    <output name="output" file="4.bed" />
+	</test>
+    </tests>
+
+    <help>
+
+**What it does**
+
+bedExtendRanges_ - extend length of entries in bed 6+ data to be at least the given length,
+taking strand directionality into account.
+
+.. _bedExtendRanges: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedExtendRanges
+
+**Usage**
+
+   bedExtendRanges database length files(s)
+
+**Example**
+
+  * bedExtendRanges -user=genome -host=genome-mysql.cse.ucsc.edu hg18 250 stdin
+
+  will transform:
+    chr1 500 525 . 100 +
+    chr1 1000 1025 . 100 -
+  to:
+    chr1 500 750 . 100 +
+    chr1 775 1025 . 100 -
+
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bigWigSummary.xml	Tue Sep 02 12:04:30 2014 -0400
@@ -0,0 +1,43 @@
+<tool id="bigWigSummary" name="bigWigSummary">
+    <description> Extract summary information from a bigWig file. </description>
+    <command> 
+	bigWigSummary $input $chrom $start $end $dataPoints -type=$type> $output
+    </command>
+    <inputs>
+        <param name="input" type="data" format="bigwig" label="Input"/>
+        <param name="chrom" type="text" value="chr" label="Chromosome" help="E.g. 'chr7'"/>
+        <param name="start" type="integer" value="" label="Start coordinate" help="BED format (0-based)."/>
+        <param name="end" type="integer" value="" label="End coordinate" help="BED format (0-based)."/>    
+        <param name="dataPoints" type="integer" value="1" label="Number of (equal) parts to break down the selected region."  help="Choose 1 for simple summary."/>
+        <param name="type" type="select" label="Operation">
+	    <option value="mean">Average value in region (default)</option>
+            <option value="min">Minimum value in region</option>
+            <option value="max">Maximum value in region</option>
+            <option value="std">Standard deviation in region</option>
+            <option value="coverage">Percentage of region that is covered</option>
+        </param>
+    </inputs>
+  
+    <outputs>
+        <data format="text" name="output"/> 
+    </outputs>
+
+    <tests>
+	<test>
+	    <param name="input" value="1.bigwig" />
+	    <param name="chrom" value="chr21" />
+	    <param name="start" value="10000000" />
+            <param name="end" value="50000000" />
+	    <param name="dataPoints" value="3" />
+	    <param name="type" value="std" />
+	    <output name="output" value="1.txt" />
+	</test>
+    <tests>
+    <help>
+
+**Usage**
+  * bigWigSummary file.bigWig chrom start end dataPoints
+  * Get summary data from bigWig for indicated region, broken into dataPoints equal parts.  (Use dataPoints=1 for simple summary.)
+
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bigwig2summary.sh	Tue Sep 02 12:04:30 2014 -0400
@@ -0,0 +1,131 @@
+#!/bin/bash
+# $Id: bigwig2summary_stdout 34 2014-02-20 08:31:20Z jens $
+
+#USE IN GALAXY
+#This script extract summary values (mean, min, max, std or coverage) from a bigwig file for a number of equal sized bins across genomic regions given in bed file.
+#If the bed file contains 6 columns (or more), column 6 is expected to contain strand information. Summary values from a negative strand will be reversed.
+
+########################################
+#bigwigSummary has 3 non-standard outputs:
+#1) n/a #(no data in bin)
+#2) no data #(no data in entire region)
+#3) <number> is not a valid option (typically if negative coordinate)
+
+#Default settings & input parsing. "" indicates required user input.
+nbins=1
+rm_header_line=0
+summary_type=mean
+
+#parse input
+while getopts hef:b:o:n:t: myarg
+do	case "$myarg" in
+	h)	echo "Usage: bigwig2summary_stdout -f <BIGWIG_FILE> -b <BED_FILE> -o <ASSEMBLY> -n <NUMBER OF BINS> -t <SUMMARY TYPE> -e"
+	        echo "Corrects for strand if bed-file has 6 columns or more. Col 6 assumed to contain strand infomation"
+		exit ;;
+	f)	bigwig_file="$OPTARG" ;;
+	b)	bed_file="$OPTARG" ;; #must be tab separated without header
+	o)	org_assembly="$OPTARG" ;;
+	n)	nbins="$OPTARG" ;;
+	t)	summary_type="$OPTARG" ;;
+	e)	rm_header_line=2 ;; #flag. if -e then first line is removed
+	[?])	echo "Usage: bigwig2summary_stdout -f <BIGWIG_FILE> -b <BED_FILE> -o <ASSEMBLY> -n <NUMBER OF BINS> -t <SUMMARY TYPE> -e"
+	        echo "Corrects for strand if bed-file has 6 columns or more. Col 6 assumed to contain strand infomation"
+		exit 1 ;;
+	esac
+done
+
+###################################################
+###VALIDATE INPUT
+###################################################
+
+#get chromosome sizes from bigwig file. bigwig file does not contain name of genome assembly.
+org_assembly_file=`mktemp -u`
+fetchChromSizes $org_assembly 2>/dev/null > $org_assembly_file
+if [ $? -ne 0 ]; then 
+  echo "ERROR: Organism genome assembly does not exist" 
+  rm $org_assembly_file
+  exit
+fi
+
+#check input bed_file. bedClip only checks first 3 columns!
+if [ `bedClip -verbose=2 <(tail -n +${rm_header_line} $bed_file) $org_assembly_file /dev/null 2>&1 | wc -l` -gt 0 ]; then
+  echo -e "ERROR: Input bed file is not in proper format!\nTry 'bedClip' to find lines causing error"
+  echo "Make sure that bigwig and bed files are using the same genome assembly"
+  exit 1
+fi
+
+#make string of "nbins" 0's to insert in regions, where no reads are found
+if [ $nbins -gt 1 ]; then
+  seq_string=`seq 1 $nbins`
+  zero_string=`printf "0\t%.s" {$seq_string} | perl -pe "s/\t$//"` 
+fi
+
+#make sure the given summary type exists
+if [ `echo $summary_type | egrep "(mean|max|min|std|coverage)" | wc -l` -ne 1 ]; then
+  echo "ERROR: Summary type must be: mean, max, min, std or coverage. Default is 'mean'"
+  exit 1
+fi
+
+#determine number of fields in bed_file
+if [ `tail -n +${rm_header_line} $bed_file | awk '{print NF}' | uniq | wc -l` -eq 1 ]; then
+  nfields_bed=`tail -n +${rm_header_line} $bed_file | awk '{print NF}' | uniq`
+else
+  echo "ERROR: Bed file does not have constant number of line columns"
+  exit 1
+fi  
+
+if [[ $nbins -gt 1 && $nfields_bed -ge 6 ]]; then
+  strand_uniq_chars=`tail -n +${rm_header_line} $bed_file | cut -f6 | sort -u | perl -pe "s/\n//"`
+  if [[ $strand_uniq_chars != "+-" && $strand_uniq_chars != "-+" ]] ; then
+    echo "ERROR: Column 6 in bed file must only contain '+' or '-' characters"
+    exit 1
+  fi
+fi 
+
+###################################################
+###EXTRACT DENSITIES FROM NORMALIZED BIGWIG FILE
+###################################################
+
+
+#if more than 1 bin AND >= 6 fields (i.e. has strand column)
+if [[ $nbins -gt 1 && $nfields_bed -ge 6 ]]; then
+
+  #cut columns 1-3+6 | rm header if flag set
+  cut -f1-3,6 $bed_file | tail -n +${rm_header_line} | while read -r line; do
+  
+    #read 4 fields into variables
+    read -r cur_chr cur_start cur_end cur_strand <<<"$line"
+    #run bigWigSummary. Combine stdout and stderr | treat exceptions and errors after 'done'
+    bigWigSummary $bigwig_file $cur_chr $cur_start $cur_end $nbins -type=${summary_type} 2>&1 | perl -pe "s/no data.+$/${zero_string}/" | awk 'BEGIN{OFS="\t"}{ if("'"$cur_strand"'"=="-") { for (i=NF; i>0; i--) { printf("%s\t",$i) } printf("\n") } else { print $0 } }'
+  done | perl -pe "s/n\/a/0/g" | perl -pe "s/^\t?0\t?$/${zero_string}/" | perl -pe "s/ +/\t/g"  | perl -pe "s/\t$//" |  sed '/^$/d'
+
+#if more than 1 bin AND less than 6 fields (i.e. no strand column)
+elif [[ $nbins -gt 1 && $nfields_bed -lt 6 ]]; then
+
+  #cut columns 1-3 | rm header if flag set
+  cut -f1-3 $bed_file | tail -n +${rm_header_line} | while read -r line; do
+  
+    #read 3 fields into variables
+    read -r cur_chr cur_start cur_end <<<"$line"
+    #run bigWigSummary. Combine stdout and stderr | treat exceptions and errors after 'done'
+    bigWigSummary $bigwig_file $cur_chr $cur_start $cur_end $nbins -type=${summary_type} 2>&1 
+  
+  done | perl -pe "s/n\/a/0/g" | perl -pe "s/no data.+$/${zero_string}/" | perl -pe "s/^\t?0\t?$/${zero_string}/" | perl -pe "s/ +/\t/g" | sed '/^$/d'
+
+
+#if 1 bin. Strand column irrelevant 
+else
+
+  cut -f1-3 $bed_file | tail -n +${rm_header_line} | while read -r line; do
+  
+    read -r cur_chr cur_start cur_end <<<"$line"
+    bigWigSummary $bigwig_file $cur_chr $cur_start $cur_end 1 -type=${summary_type} 2>&1
+    
+  done | perl -pe "s/no data.+$/0/" | perl -pe "s/n\/a/0/g" | sed '/^$/d'
+  
+fi 
+  
+
+
+  
+  
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bigwig2summary.xml	Tue Sep 02 12:04:30 2014 -0400
@@ -0,0 +1,104 @@
+<tool id="bigwig2_summary" name="bigWig2Summary">
+    <description> Extract summary information from a bigWig file across multiple genomic regions specified by the user. </description>
+    <requirements>
+        <requirement type="package" version="1.0">bigWigSummary</requirement>
+        <requirement type="package" version="1.0">fetchChromSizes</requirement>
+        <requirement type="package" version="1.0">bedClip</requirement>
+    </requirements>
+    <command interpreter="bash"> 
+	bigwig2summary.sh -f $input_bw -b $input_bed -n $bins -o $assembly -t $type $header > $output
+    </command>
+    <inputs>
+        <param name="input_bw" type="data" format="bigwig" label="Extract summary from" help="bigWig format."/>
+        <param name="input_bed" type="data" format="tabular" label="using genomic regions in" help="TAB delimited BED-like file."/>
+        <param name="bins" type="integer" value="1" label="Number of bins" help="Postitive integer"/>
+        <param name="assembly" type="text" label="Orgamism assembly" help="E.g. hg19" />
+        <param name="header" type="boolean" checked="False" truevalue="-e" falsevalue=" " label="Does the genomic region file contain a header?" />    
+        <param name="type" type="select" label="Operation" help="">
+	    <option value="mean">Average value in region (default)</option>
+            <option value="min">Minimum value in region</option>
+            <option value="max">Maximum value in region</option>
+            <option value="std">Standard deviation in region</option>
+            <option value="coverage">Percentage of region that is covered</option>
+        </param>
+    </inputs>
+  
+    <outputs>
+        <data format="tabular" name="output"/> 
+    </outputs>
+
+    <tests>
+        <test>
+	    <param name="input_bw" value="1.bigwig" />
+	    <param name="input_bed" value="1.bed" />
+	    <param name="bins" value="3" />
+	    <param name="assembly" value="hg19" />
+	    <output name="output" file="1.tabular" />
+        </test>
+        <test>
+            <param name="input_bw" value="1.bigwig" />
+            <param name="input_bed" value="2.bed" />
+            <param name="bins" value="5" />
+            <param name="assembly" value="hg19" />
+            <output name="output" file="2.tabular" />
+        </test>
+    </tests>
+
+    <help>
+
+This tool extracts summary values (mean, min, max, std or coverage) from a **bigWig** file for a number of equal sized bins across genomic regions given in an a "BED-like" file.
+
+The script this tool is based on is written by Jens Vilstrup Johansen and uses bigWigSummary_, bedClip_ and fetchChromSizes_.
+
+.. _bigWigSummary: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary 
+
+.. _bedClip: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip
+
+-- _fetchChromSizes: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes
+
+-----
+
+.. class:: infomark
+
+The file contaning the genomic region must be TAB-delimited with at list 3 columns representing Chromosome, ChrStart and ChrEnd. If the file contains 6 columns (or more), column 6 is expected to contain strand information. Summary values from a negative strand will be reversed.
+ 
+-----
+
+**Example 1**
+
+Input BED file::
+
+  chr19   50178708        50180708
+  chr6    90348174        90350174
+  chr16   58495848        58497848
+  chr5    180580242       180582242
+  chr9    120177017       120179017  
+
+Extract summary (*#* of bins = 3):: 
+
+  0		0		0
+  0.144886	0		0
+  0.507327	1.14649		1.38456
+  0.221471	0.144886	0.309857
+  0.348944	0.426638	0.244495
+
+**Example 2**
+
+Input BED file (with strand information)::
+
+  chr19	  50178708	50180708	NM_198318	0	+	PRMT1
+  chr6	  90348174	90350174	NM_020466	0	-	LYRM2
+  chr16	  58495848	58497848	NM_020465	0	+	NDRG4
+  chr5 	  180580242	180582242	NM_206880	0	+	OR2V2
+  chr9    120177017     120179017       NM_014010       0       -	ASTN2
+
+Extract summary (*#* of bins = 3)::
+
+  0		0		0
+  0		0		0.144886
+  0.507327	1.14649		1.38456
+  0.221471	0.144886	0.309857
+  0.244495	0.426638	0.348944
+
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.bed	Tue Sep 02 12:04:30 2014 -0400
@@ -0,0 +1,5 @@
+chr19	50178708	50180708
+chr6	90348174	90350174
+chr16	58495848	58497848
+chr5	180580242	180582242
+chr9	120177017	120179017
Binary file test-data/1.bigwig has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.tabular	Tue Sep 02 12:04:30 2014 -0400
@@ -0,0 +1,4 @@
+0.144886	0	0
+0.507327	1.14649	1.38456
+0.221471	0.144886	0.309857
+0.348944	0.426638	0.244495
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.txt	Tue Sep 02 12:04:30 2014 -0400
@@ -0,0 +1,1 @@
+0.796113	0.273952	0.437672
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.bed	Tue Sep 02 12:04:30 2014 -0400
@@ -0,0 +1,5 @@
+chr19	50178708	50180708	NM_198318	0	+	PRMT1
+chr6	90348174	90350174	NM_020466	0	-	LYRM2
+chr16	58495848	58497848	NM_020465	0	+	NDRG4
+chr5	180580242	180582242	NM_206880	0	+	OR2V2
+chr9	120177017	120179017	NM_014010	0	-	ASTN2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.tabular	Tue Sep 02 12:04:30 2014 -0400
@@ -0,0 +1,4 @@
+0	0	0	0.144886	0
+0.396878	0.970009	1.1091	1.17538	1.40612
+0.203829	0.21262	0.144886	0.409996	0.274558
+0.180424	0.430989	0.458898	0.35171	0.307157
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3.bed	Tue Sep 02 12:04:30 2014 -0400
@@ -0,0 +1,7 @@
+chr19	50178708	50180708
+chr21	48119895	48139895
+chr6	90348174	90350174
+chr16	58495848	58497848
+chr5	180580242	180582242
+chr17	81194210	81196210
+chr9	120177017	120179017  
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/4.bed	Tue Sep 02 12:04:30 2014 -0400
@@ -0,0 +1,5 @@
+chr19 50178708 50183708 NM_198318 0 + PRMT1
+chr6 90345174 90350174 NM_020466 0 - LYRM2
+chr16 58495848 58500848 NM_020465 0 + NDRG4
+chr5 180580242 180585242 NM_206880 0 + OR2V2
+chr9 120174017 120179017 NM_014010 0 - ASTN2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Sep 02 12:04:30 2014 -0400
@@ -0,0 +1,71 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="bigWigSummary" version="1.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary</action>
+	        <action type="move_directory_files">
+        	    <source_directory>.</source_directory>
+        	    <destination_directory>$INSTALL_DIR</destination_directory>
+        	</action>
+                <action type="chmod"><file mode="755">$INSTALL_DIR/bigWigSummary</file></action>
+		<action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+	    </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+    <package name="bedClip" version="1.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedClip</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+                <action type="chmod"><file mode="755">$INSTALL_DIR/bedClip</file></action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+    <package name="bedExtendRanges" version="1.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedExtendRanges</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+                <action type="chmod"><file mode="755">$INSTALL_DIR/bedExtendRanges</file></action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+    <package name="fetchChromSizes" version="1.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+		<action type="chmod"><file mode="755">$INSTALL_DIR/fetchChromSizes</file></action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        </readme>
+    </package>
+</tool_dependency>