# HG changeset patch
# User iuc
# Date 1442951480 14400
# Node ID 6fe93c81bcd0918dcae56989bec11aafb5fd23c9
# Parent  0eaccc10220ca61d612340c61df856f57fcfd210
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_python_2_7_deeptools_1_5_11 commit 743caa3d7198c38c8f3d9f90e4aae16f76cfd7f2-dirty

diff -r 0eaccc10220c -r 6fe93c81bcd0 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Sep 22 07:17:28 2015 -0400
+++ b/tool_dependencies.xml	Tue Sep 22 15:51:20 2015 -0400
@@ -19,7 +19,7 @@
         <repository changeset_revision="ed5fdaba090a" 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="312">
-        <repository changeset_revision="34e9010db346" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="ceda74761368" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="python" version="2.7.10">
         <repository changeset_revision="08162f8bc496" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
@@ -30,13 +30,10 @@
                 <action type="setup_python_environment">
                    <repository changeset_revision="08162f8bc496" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="python" version="2.7.10" />
-                   </repository>
+                    </repository>
                     <repository changeset_revision="dd8ace13f3aa" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="pysam" version="0.8.3" />
                     </repository>
-                    <repository changeset_revision="ed5fdaba090a" name="package_python_2_7_bx_python_0_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="bx-python" version="0.7.2" />
-                    </repository>
                     <repository changeset_revision="8d42102c4e36" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="numpy" version="1.9" />
                     </repository>
@@ -46,10 +43,13 @@
                     <repository changeset_revision="7002d3382856" name="package_python_2_7_scipy_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="scipy" version="0.14" />
                     </repository>
+                    <repository changeset_revision="ed5fdaba090a" name="package_python_2_7_bx_python_0_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="bx-python" version="0.7.2" />
+                    </repository>
                     <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="samtools" version="0.1.19" />
                     </repository>
-                    <repository changeset_revision="34e9010db346" name="package_ucsc_tools_312" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="ceda74761368" name="package_ucsc_tools_312" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="ucsc_tools" version="312" />
                     </repository>
                     <package>https://github.com/fidelram/deepTools/archive/1.5.11.tar.gz</package>
@@ -61,24 +61,6 @@
                     <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>
                     <!-- libpng lib path -->
                     <environment_variable action="set_to" name="LIBPNG_LIB_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable>
                     <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable>