Mercurial > repos > scottx611x > cooler_convert

changeset 5:4543c0fdd563 draft

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planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
author scottx611x
date Sun, 20 Nov 2016 20:25:45 -0500
parents b51c0906bc8b
children 0a8070066879
files recursive_agg_onefile.py tool_dependencies.xml tool_dependencies.xml.old
diffstat 3 files changed, 59 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/recursive_agg_onefile.py	Sun Nov 20 19:54:19 2016 -0500
+++ b/recursive_agg_onefile.py	Sun Nov 20 20:25:45 2016 -0500
@@ -3,7 +3,9 @@
 import argparse
 import sys
 
-import numpy as npr
+import numpy as np
+from cooler.io import CoolerAggregator
+import cooler.ice
 import cooler
 import h5py
 
--- a/tool_dependencies.xml	Sun Nov 20 19:54:19 2016 -0500
+++ b/tool_dependencies.xml	Sun Nov 20 20:25:45 2016 -0500
@@ -1,22 +1,50 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <package name="numpy" version="1.9">
+        <repository changeset_revision="5f2b261ffc5b" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
     <package name="python" version="2.7.10">
         <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="cooler" version="0.5.3">
+    <package name="pandas" version="0.16">
         <install version="1.0">
             <actions>
                 <action type="setup_python_environment">
-                    <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="python" version="2.7.10" />
+                   <repository changeset_revision="a28e3c30828d" 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="5f2b261ffc5b" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.9" />
                     </repository>
-                    <!-- Just download from pypi -->
-                    <package md5sum="f95024c8c201df01fbaa2de10d81edd3">https://pypi.python.org/packages/64/6e/8ed3ba753e269e0cb393ce8898292e4540a763f155bf6cf855b454dbbd2a/cooler-0.5.3.tar.gz</package>
+                    <!-- allow downloading and installing an Python package from https://pypi.org/ -->
+                    <package sha256sum="8d9b7ad4fadf9648acc924a6ee522c7cb5b474e75faaad9d90dfd55e2805b495">
+                        https://pypi.python.org/packages/source/B/Bottleneck/Bottleneck-1.0.0.tar.gz
+                    </package>
+                    <package sha256sum="99266ef30a37e43932deec2b7ca73e83c8dbc3b9ff703ec73eca6b1dae6befea">
+                        https://pypi.python.org/packages/source/p/pytz/pytz-2015.7.tar.gz
+                    </package>
+                    <package sha256sum="105f8d68616f8248e24bf0e9372ef04d3cc10104f1980f54d57b2ce73a5ad56a">https://pypi.python.org/packages/source/s/six/six-1.10.0.tar.gz</package>
+                    <package sha256sum="3e95445c1db500a344079a47b171c45ef18f57d188dffdb0e4165c71bea8eb3d">
+                        https://pypi.python.org/packages/source/p/python-dateutil/python-dateutil-2.4.2.tar.gz
+                    </package>
+                    <package sha256sum="e01853dfe111f3aea005315573400b7216ddbabbf1f28d482a71217d67ae4f81">
+                        https://pypi.python.org/packages/source/p/pandas/pandas-0.16.2.tar.gz
+                    </package>
                 </action>
+
                 <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
+                    <environment_variable action="set_to" name="PYTHONPATH_PANDAS">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="PANDAS_ROOT_PATH">$INSTALL_DIR</environment_variable>
                 </action>
             </actions>
         </install>
+        <readme>
+            Pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language.
+            The PYTHONPATH for pandas can be accessed through PYTHONPATH_PANDAS.
+            http://pandas.pydata.org/
+        </readme>
     </package>
 </tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml.old	Sun Nov 20 20:25:45 2016 -0500
@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="python" version="2.7.10">
+        <repository name="package_python_2_7_10" owner="iuc" prior_installation_required="True" />
+    </package>
+    <package name="cooler" version="0.5.3">
+        <install version="1.0">
+            <actions>
+                <action type="setup_python_environment">
+                    <repository name="package_python_2_7_10" owner="iuc">
+                        <package name="python" version="2.7.10" />
+                    </repository>
+                    <!-- Just download from pypi -->
+                    <package md5sum="f95024c8c201df01fbaa2de10d81edd3">https://pypi.python.org/packages/64/6e/8ed3ba753e269e0cb393ce8898292e4540a763f155bf6cf855b454dbbd2a/cooler-0.5.3.tar.gz</package>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+    </package>
+</tool_dependency>