Mercurial > repos > iuc > package_python_2_7_deeptools_1_5_11

changeset 0:315b83e21eea draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 16:58:29 -0400
parents
children 01eb49da8dcf
files tool_dependencies.xml
diffstat 1 files changed, 95 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Oct 19 16:58:29 2015 -0400
@@ -0,0 +1,95 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="numpy" version="1.9">
+        <repository changeset_revision="b4b823ad5f0f" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="matplotlib" version="1.4">
+        <repository changeset_revision="8f39fc9cadb1" name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="scipy" version="0.14">
+        <repository changeset_revision="f9a80a69d278" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pysam" version="0.8.3">
+        <repository changeset_revision="ee642ed79a3b" name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bx-python" version="0.7.2">
+        <repository changeset_revision="8b54b30f3cd4" name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="ucsc_tools" version="312">
+        <repository changeset_revision="2d6bafd63401" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="python" version="2.7.10">
+        <repository changeset_revision="b1a672a0df3c" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.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="b1a672a0df3c" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                       <package name="python" version="2.7.10" />
+                   </repository>
+                    <repository changeset_revision="ee642ed79a3b" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="pysam" version="0.8.3" />
+                    </repository>
+                    <repository changeset_revision="8b54b30f3cd4" name="package_python_2_7_bx_python_0_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="bx-python" version="0.7.2" />
+                    </repository>
+                    <repository changeset_revision="b4b823ad5f0f" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.9" />
+                    </repository>
+                    <repository changeset_revision="8f39fc9cadb1" name="package_python_2_7_matplotlib_1_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="matplotlib" version="1.4" />
+                    </repository>
+                    <repository changeset_revision="f9a80a69d278" name="package_python_2_7_scipy_0_14" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="scipy" version="0.14" />
+                    </repository>
+                    <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="samtools" version="0.1.19" />
+                    </repository>
+                    <repository changeset_revision="2d6bafd63401" name="package_ucsc_tools_312" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="ucsc_tools" version="312" />
+                    </repository>
+                    <package>https://github.com/fidelram/deepTools/archive/1.5.11.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>
+                    <!-- 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>
+                    <!-- 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>