--- a/bamCompare.xml	Mon Feb 03 18:31:42 2014 -0500
+++ b/bamCompare.xml	Tue Feb 04 03:38:20 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamCompare" name="bamCompare" version="1.0.3">
+<tool id="deeptools_bamCompare" name="bamCompare" version="1.0.4">
     <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig)</description>
     <expand macro="requirements" />
     <expand macro="stdio" />

--- a/bamCorrelate.xml	Mon Feb 03 18:31:42 2014 -0500
+++ b/bamCorrelate.xml	Tue Feb 04 03:38:20 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamCorrelate" name="bamCorrelate" version="1.0.3">
+<tool id="deeptools_bamCorrelate" name="bamCorrelate" version="1.0.4">
     <description>correlates pairs of BAM files</description>
     <expand macro="requirements" />
     <expand macro="stdio" />

--- a/bamCoverage.xml	Mon Feb 03 18:31:42 2014 -0500
+++ b/bamCoverage.xml	Tue Feb 04 03:38:20 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.3">
+<tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.4">
     <description> generates a coverage bigWig file from a given BAM file.  Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description>
     <expand macro="requirements" />
     <expand macro="stdio" />

--- a/bamFingerprint.xml	Mon Feb 03 18:31:42 2014 -0500
+++ b/bamFingerprint.xml	Tue Feb 04 03:38:20 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0.3">
+<tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0.4">
     <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
     <expand macro="requirements" />
     <expand macro="stdio" />

--- a/computeGCBias.xml	Mon Feb 03 18:31:42 2014 -0500
+++ b/computeGCBias.xml	Tue Feb 04 03:38:20 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.3">
+<tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.4">
     <description>to see whether your samples should be normalized for GC bias</description>
     <expand macro="requirements" />
     <expand macro="stdio" />

--- a/computeMatrix.xml	Mon Feb 03 18:31:42 2014 -0500
+++ b/computeMatrix.xml	Tue Feb 04 03:38:20 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0.3">
+<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0.4">
     <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
     <expand macro="requirements" />
     <expand macro="stdio" />

--- a/correctGCBias.xml	Mon Feb 03 18:31:42 2014 -0500
+++ b/correctGCBias.xml	Tue Feb 04 03:38:20 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.3">
+<tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.4">
     <description>uses the output from computeGCBias to generate corrected BAM files</description>
     <expand macro="requirements" />
     <expand macro="stdio" />

--- a/deepTools_macros.xml	Mon Feb 03 18:31:42 2014 -0500
+++ b/deepTools_macros.xml	Tue Feb 04 03:38:20 2014 -0500
@@ -50,7 +50,7 @@
             <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
             <requirement type="package" >ucsc_tools</requirement>
-            <requirement type="package" version="1.5.4_1093b2d281576f23ee04740bd5eae3f7b8422f7e">deepTools</requirement>
+            <requirement type="package" version="1.5.4_3268f7e1458f3a520ab6fea3039971ee9d7a6d5b">deepTools</requirement>
             <requirement type="package" version="0.1">ucsc_tools</requirement>
             <requirement type="package" version="1.7.1">numpy</requirement>
             <requirement type="package" version="0.7.7">pysam</requirement>

--- a/heatmapper.xml	Mon Feb 03 18:31:42 2014 -0500
+++ b/heatmapper.xml	Tue Feb 04 03:38:20 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_heatmapper" name="heatmapper" version="1.0.3">
+<tool id="deeptools_heatmapper" name="heatmapper" version="1.0.4">
     <description>creates a heatmap for a score associated to genomic regions</description>
     <expand macro="requirements"/>
     <expand macro="stdio" />

--- a/profiler.xml	Mon Feb 03 18:31:42 2014 -0500
+++ b/profiler.xml	Tue Feb 04 03:38:20 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_profiler" name="profiler" version="1.0.3">
+<tool id="deeptools_profiler" name="profiler" version="1.0.4">
     <description>
         creates a profile plot for a score associated to genomic regions
     </description>

--- a/tool_dependencies.xml	Mon Feb 03 18:31:42 2014 -0500
+++ b/tool_dependencies.xml	Tue Feb 04 03:38:20 2014 -0500
@@ -57,7 +57,7 @@
          <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
      </package>
 
-    <package name="deepTools" version="1.5.4_1093b2d281576f23ee04740bd5eae3f7b8422f7e">
+    <package name="deepTools" version="1.5.4_3268f7e1458f3a520ab6fea3039971ee9d7a6d5b">
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
@@ -79,7 +79,7 @@
                         <package name="scipy" version="0.12.0" />
                     </repository>
                 </action>
-                <action type="shell_command">git reset --hard 1093b2d281576f23ee04740bd5eae3f7b8422f7e</action>
+                <action type="shell_command">git reset --hard 3268f7e1458f3a520ab6fea3039971ee9d7a6d5b</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;