Mercurial > repos > bgruening > deeptools

changeset 9:73761f33f198 draft

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Uploaded
author bgruening
date Tue, 17 Sep 2013 10:27:29 -0400
parents b4ed2153f75c
children a68a771625d2
files bamCompare.xml bamCorrelate.xml bamCoverage.xml bamFingerprint.xml bigwigCompare.xml computeGCBias.xml computeMatrix.xml correctGCBias.xml heatmapper.xml profiler.xml tool_dependencies.xml
diffstat 11 files changed, 12 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/bamCompare.xml	Tue Sep 17 08:44:51 2013 -0400
+++ b/bamCompare.xml	Tue Sep 17 10:27:29 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="deeptools_bamCompare" name="bamCompare" version="1.0">
   <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference.</description>
   <requirements>
-    <requirement type="package" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">deepTools</requirement>
+    <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
     <requirement type="package" version="0.1">ucsc_tools</requirement>
     <requirement type="package" >deepTools</requirement>
--- a/bamCorrelate.xml	Tue Sep 17 08:44:51 2013 -0400
+++ b/bamCorrelate.xml	Tue Sep 17 10:27:29 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="deeptools_bamCorrelate" name="bamCorrelate" version="1.0.1">
   <description>correlates pairs of BAM files</description>
   <requirements>
-    <requirement type="package" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">deepTools</requirement>
+    <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement>
     <requirement type="package" >deepTools</requirement>
   </requirements>
   <command>
--- a/bamCoverage.xml	Tue Sep 17 08:44:51 2013 -0400
+++ b/bamCoverage.xml	Tue Sep 17 10:27:29 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0">
   <description> generates a coverage bigWig file from a given BAM file.  Multiple options are available to count reads and normalize coverage.</description>
   <requirements>
-    <requirement type="package" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">deepTools</requirement>
+    <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement>
     <requirement type="package" version="0.1">ucsc_tools</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
     <requirement type="package" >deepTools</requirement>
--- a/bamFingerprint.xml	Tue Sep 17 08:44:51 2013 -0400
+++ b/bamFingerprint.xml	Tue Sep 17 10:27:29 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0">
   <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
   <requirements>
-    <requirement type="package" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">deepTools</requirement>
+    <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement>
     <requirement type="package" >deepTools</requirement>
   </requirements>
   <command>
--- a/bigwigCompare.xml	Tue Sep 17 08:44:51 2013 -0400
+++ b/bigwigCompare.xml	Tue Sep 17 10:27:29 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="deeptools_bigwigCompare" name="bigwigCompare" version="1.0">
   <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</description>
   <requirements>
-    <requirement type="package" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">deepTools</requirement>
+    <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement>
     <requirement type="package" version="0.1">ucsc_tools</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
     <requirement type="package" >deepTools</requirement>
--- a/computeGCBias.xml	Tue Sep 17 08:44:51 2013 -0400
+++ b/computeGCBias.xml	Tue Sep 17 10:27:29 2013 -0400
@@ -2,7 +2,7 @@
   <description>to see whether your samples should be normalized for GC bias</description>
   
   <requirements>
-    <requirement type="package" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">deepTools</requirement>
+    <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement>
     <requirement type="package" >deepTools</requirement>
   </requirements>
   <stdio>
--- a/computeMatrix.xml	Tue Sep 17 08:44:51 2013 -0400
+++ b/computeMatrix.xml	Tue Sep 17 10:27:29 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0">
   <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>
   <requirements>
-    <requirement type="package" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">deepTools</requirement>
+    <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement>
     <requirement type="package" >deepTools</requirement>
   </requirements>
   <command>
--- a/correctGCBias.xml	Tue Sep 17 08:44:51 2013 -0400
+++ b/correctGCBias.xml	Tue Sep 17 10:27:29 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.1">
   <description>uses the output from computeGCBias to generate corrected BAM files</description>
   <requirements>
-    <requirement type="package" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">deepTools</requirement>
+    <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement>
     <requirement type="package" version="0.1">ucsc_tools</requirement>
     <requirement type="package" >deepTools</requirement>
   </requirements>
--- a/heatmapper.xml	Tue Sep 17 08:44:51 2013 -0400
+++ b/heatmapper.xml	Tue Sep 17 10:27:29 2013 -0400
@@ -7,7 +7,7 @@
     <requirement type="package" version="1.2.1">matplotlib</requirement>
     <requirement type="package" version="0.12.0">scipy</requirement>
     <requirement type="package" version="0.1">ucsc_tools</requirement>
-    <requirement type="package" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">deepTools</requirement>
+    <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement>
     <requirement type="package" >deepTools</requirement>
   </requirements>
 
--- a/profiler.xml	Tue Sep 17 08:44:51 2013 -0400
+++ b/profiler.xml	Tue Sep 17 10:27:29 2013 -0400
@@ -3,7 +3,7 @@
     creates a profile plot for a score associated to genomic regions
   </description>
   <requirements>
-    <requirement type="package" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">deepTools</requirement>
+    <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement>
     <requirement type="package" >deepTools</requirement>
   </requirements>
   <command>
--- a/tool_dependencies.xml	Tue Sep 17 08:44:51 2013 -0400
+++ b/tool_dependencies.xml	Tue Sep 17 10:27:29 2013 -0400
@@ -45,11 +45,11 @@
          <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="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">
+    <package name="deepTools" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
-                <action type="shell_command">git reset --hard df852fa1ef13251a17274ee18fbf919fbc515079</action>
+                <action type="shell_command">git reset --hard 3e13687c89e951476776b15afb4bbbc3b906f761</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;