Mercurial > repos > iuc > package_python_2_7_deeptools_1_5_11

diff tool_dependencies.xml @ 6:b89f7737e36a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_python_2_7_deeptools_1_5_11 commit d094788c200e3ecf24f2a429000c888e82131ed1
author iuc
date Mon, 19 Oct 2015 16:52:52 -0400
parents ff7a945199fa
children b8c2066c4620
line wrap: on
line diff
--- a/tool_dependencies.xml	Sat Oct 10 08:11:28 2015 -0400
+++ b/tool_dependencies.xml	Mon Oct 19 16:52:52 2015 -0400
@@ -7,45 +7,45 @@
         <repository changeset_revision="da6c5de0d919" 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="f420f862153e" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="d5d011480b68" 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="10a6799b6a27" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="cf38050e2c04" 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="dcdd1f49dfd4" 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="78c115f001ee" name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="6a1dc79b73d4" 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="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="4f81728216e7" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="b9171d06f311" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="deepTools" version="1.5.11">
         <install version="1.0">
             <actions>
                 <action type="setup_python_environment">
-                    <repository changeset_revision="4f81728216e7" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="python" version="2.7.10" />
-                    </repository>
+                   <repository changeset_revision="b9171d06f311" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                       <package name="python" version="2.7.10" />
+                   </repository>
                     <repository changeset_revision="dcdd1f49dfd4" 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="6a1dc79b73d4" 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="da6c5de0d919" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="numpy" version="1.9" />
                     </repository>
-                    <repository changeset_revision="f420f862153e" name="package_python_2_7_matplotlib_1_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="d5d011480b68" name="package_python_2_7_matplotlib_1_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="matplotlib" version="1.4" />
                     </repository>
-                    <repository changeset_revision="10a6799b6a27" name="package_python_2_7_scipy_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="cf38050e2c04" 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="78c115f001ee" 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>
@@ -61,6 +61,24 @@
                     <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>