diff tool_dependencies.xml @ 48:72d1d7c68bd3 draft

Uploaded

--- a/tool_dependencies.xml	Tue Apr 01 12:31:58 2014 -0400
+++ b/tool_dependencies.xml	Tue Aug 26 13:48:56 2014 -0400
@@ -1,22 +1,22 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="36aa94676939" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="numpy" version="1.7.1">
-        <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="matplotlib" version="1.2.1">
-        <repository changeset_revision="85b7ddf90888" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="de9c362fb3f2" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="scipy" version="0.12.0">
-        <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a983dc7c8103" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="pysam" version="0.7.7">
-        <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="bx-python" version="12-2013">
-        <repository changeset_revision="5457e32b427c" name="package_bx_python_12_2013" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="5457e32b427c" name="package_bx_python_12_2013" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 
     <package name="ucsc_tools" version="0.1">
@@ -57,29 +57,29 @@
          <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="1.5.8_09023018b96c23f922aa2ea553090e9df8ecf41e">
+    <package name="deepTools" version="1.5.8.2">
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="pysam" version="0.7.7" />
                     </repository>
-                    <repository changeset_revision="5457e32b427c" name="package_bx_python_12_2013" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="5457e32b427c" name="package_bx_python_12_2013" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="bx-python" version="12-2013" />
                     </repository>
-                    <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="numpy" version="1.7.1" />
                     </repository>
-                    <repository changeset_revision="85b7ddf90888" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="de9c362fb3f2" name="package_matplotlib_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="matplotlib" version="1.2.1" />
                     </repository>
-                    <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="a983dc7c8103" name="package_scipy_0_12" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="scipy" version="0.12.0" />
                     </repository>
                 </action>
-                <action type="shell_command">git reset --hard 09023018b96c23f922aa2ea553090e9df8ecf41e</action>
+                <action type="shell_command">git reset --hard ae9c18b3b7e79d0d1077f636168ac24baeb7b184</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;