Mercurial > repos > scottx611x > cooler_convert

changeset 30:f4eb283011a7 draft

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planemo upload commit 9e980862c8b763cf3dd0209be49f0d2d75a90614-dirty
author scottx611x
date Mon, 21 Nov 2016 16:37:04 -0500
parents 382c372800e1
children b35821db18e8
files recursive_agg_onefile.xml tool_dependencies.xml tool_dependencies.xml.old
diffstat 3 files changed, 34 insertions(+), 34 deletions(-) [+]
line wrap: on
line diff
--- a/recursive_agg_onefile.xml	Mon Nov 21 15:41:57 2016 -0500
+++ b/recursive_agg_onefile.xml	Mon Nov 21 16:37:04 2016 -0500
@@ -1,7 +1,7 @@
 
 <tool id="recursive_agg_cooler" name="Generate Multi-res Cooler File" version="1.0.0">
   <description>Recursively aggregate a single resolution cooler file into a multi-resolution file.</description>
-  <command> /usr/bin/python $__tool_directory__/recursive_agg_onefile.py $input --out $output</command>
+  <command interpreter="python">$__tool_directory__/recursive_agg_onefile.py $input --out $output</command>
   <inputs>
     <param format="h5" name="input" type="data" label="Source cooler file"/>
   </inputs>
--- a/tool_dependencies.xml	Mon Nov 21 15:41:57 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-	<package name="numpy" version="1.9">
-		<repository changeset_revision="5f2b261ffc5b" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-	</package>
-	<package name="scipy" version="0.14">
-		<repository changeset_revision="1481a40ab1d1" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-	</package>
-	<package name="setuptools" version="19.0">
-        <repository changeset_revision="c0a6821af233" name="package_setuptools_19_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package> 
-	<package name="cooler" version="0.5.3">
-        <install version="1.0">
-            <actions>
-            	<action md5="f95024c8c201df01fbaa2de10d81edd3" type="download_by_url">https://pypi.python.org/packages/64/6e/8ed3ba753e269e0cb393ce8898292e4540a763f155bf6cf855b454dbbd2a/cooler-0.5.3.tar.gz</action>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="c0a6821af233" name="package_setuptools_19_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="setuptools" version="19.0" />
-                    </repository>
-                </action>
-                <action type="make_directory">$INSTALL_DIR/lib/python</action>
-                <action type="shell_command">
-                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
-                    python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-		    </actions>
-        </install>
-	</package>
-</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml.old	Mon Nov 21 16:37:04 2016 -0500
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="numpy" version="1.9">
+		<repository name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" />
+	</package>
+	<package name="scipy" version="0.14">
+		<repository name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" />
+	</package>
+	<package name="setuptools" version="19.0">
+        <repository name="package_setuptools_19_0" owner="iuc" prior_installation_required="True"/>
+    </package> 
+	<package name="cooler" version="0.5.3">
+        <install version="1.0">
+            <actions>
+            	<action type="download_by_url" md5="f95024c8c201df01fbaa2de10d81edd3">https://pypi.python.org/packages/64/6e/8ed3ba753e269e0cb393ce8898292e4540a763f155bf6cf855b454dbbd2a/cooler-0.5.3.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository name="package_setuptools_19_0" owner="iuc">
+                        <package name="setuptools" version="19.0" />
+                    </repository>
+                </action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="shell_command">
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
+                    python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+		    </actions>
+        </install>
+	</package>
+</tool_dependency>