# HG changeset patch
# User iuc
# Date 1432435664 14400
# Node ID 2cfa2cdcdf796603ac448bdc3a213899c9291673
# Parent  352cfe69d08e39786790b112ff4e556e4d51c094
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_python_2_7_deeptools_1_5_10 commit 0d7fcf576fd797327af90538b216473ef13daa41

diff -r 352cfe69d08e -r 2cfa2cdcdf79 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat May 23 15:05:34 2015 -0400
+++ b/tool_dependencies.xml	Sat May 23 22:47:44 2015 -0400
@@ -1,6 +1,93 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="numpy" version="1.9">
+        <repository changeset_revision="baf8064f280c" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="matplotlib" version="1.4">
+        <repository changeset_revision="513b3bf6cdc3" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="scipy" version="0.14">
+        <repository changeset_revision="c482361097f5" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pysam" version="0.8.3">
+        <repository changeset_revision="b1cd8e8b8346" name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bx-python" version="0.7.2">
+        <repository changeset_revision="15a0f73e1325" name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ucsc_tools" version="0.1">
+        <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="python" version="2.7">
+        <repository changeset_revision="00d2c3e43807" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
     <package name="deepTools" version="1.5.10">
-        <repository changeset_revision="dfbd18874c87" name="package_python_2_7_deeptools_1_5_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
+        <install version="1.0">
+            <actions>
+                <action type="setup_python_environment">
+                   <repository changeset_revision="00d2c3e43807" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                       <package name="python" version="2.7" />
+                   </repository>
+                    <repository changeset_revision="b1cd8e8b8346" name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="pysam" version="0.8.3" />
+                    </repository>
+                    <repository changeset_revision="15a0f73e1325" name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="bx-python" version="0.7.2" />
+                    </repository>
+                    <repository changeset_revision="baf8064f280c" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.9" />
+                    </repository>
+                    <repository changeset_revision="513b3bf6cdc3" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="matplotlib" version="1.4" />
+                    </repository>
+                    <repository changeset_revision="c482361097f5" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="scipy" version="0.14" />
+                    </repository>
+                    <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="samtools" version="0.1.19" />
+                    </repository>
+                    <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="ucsc_tools" version="0.1" />
+                    </repository>
+                    <package>https://github.com/fidelram/deepTools/archive/1.5.10.tar.gz</package>
+                </action>
+
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="DEEPTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="DEEPTOOLS_PYTHONPATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="DEEPTOOLS_PATH">$INSTALL_DIR/bin</environment_variable>
+                    <!-- include samtools into PATH -->
+                    <environment_variable action="prepend_to" name="PATH">$ENV[BAM_ROOT]/bin</environment_variable>
+                    <!-- include numpy -->
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
+                    <!-- include matplotlib -->
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
+                    <!-- include scipy -->
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable>
+                    <!-- include bx-python -->
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_BX_PYTHON]</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_BX_PYTHON]</environment_variable>
+                    <!-- include pysam -->
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_PYSAM]</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_PYSAM]</environment_variable>
+                    <!-- include ucsc tools -->
+                    <environment_variable action="prepend_to" name="PATH">$ENV[UCSC_TOOLS_ROOT_PATH]</environment_variable>
+
+                    <!-- disable the config file of deepTools -->
+                    <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
+                </action>
+             </actions>
+         </install>
+         <readme>
+            Installation of deepTools from Fidel Ramirez.
+            https://github.com/fidelram/deepTools
+         </readme>
+     </package>
 </tool_dependency>