Mercurial > repos > mzeidler > virana

changeset 30:3cee6b37cdcf draft

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Uploaded
author mzeidler
date Mon, 23 Sep 2013 09:19:22 -0400
parents 5e938e5eb46f
children e6fb8ee52507
files tool_dependencies.xml
diffstat 1 files changed, 25 insertions(+), 31 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Sep 23 08:57:57 2013 -0400
+++ b/tool_dependencies.xml	Mon Sep 23 09:19:22 2013 -0400
@@ -1,4 +1,10 @@
 <tool_dependency>
+    <package name="numpy" version="1.7.1">
+       <repository changeset_revision="b7ff4a8c58df" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="freetype" version="2.4.11">
+        <repository changeset_revision="fe5cfaf931ff" name="package_freetype_2_4" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
     <package name="virana_python" version="1.0">
         <install version="1.0">
             <actions>
@@ -8,24 +14,15 @@
             </actions>
         </install>
     </package>
- <package name="numpy" version="1.7.1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://pypi.python.org/packages/source/n/numpy/numpy-1.7.1.tar.gz</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 --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
-                <action type="set_environment">
-                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
-                    <environment_variable name="PYTHONPATH_NUMPY" action="set_to">$INSTALL_DIR/lib/python</environment_variable>
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-    </package>
 <package name="biopython" version="1.61">
         <install version="1.0">
             <actions>
                 <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="b7ff4a8c58df" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.7.1" />
+                    </repository>
+                </action>    
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
@@ -42,27 +39,19 @@
             </actions>
         </install>
     </package>
-    <package name="freetype" version="2.4.11">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/freetype/freetype2/2.4.11/freetype-2.4.11.tar.bz2</action>
-                <action type="shell_command">./configure --prefix=$INSTALL_DIR/freetype/</action>
-                <action type="shell_command">make</action>
-                <action type="shell_command">make install</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="append_to">$INSTALL_DIR/freetype/bin/</environment_variable>
-                    <environment_variable name="FREETYPE_LIB_DIR" action="set_to">$INSTALL_DIR/freetype/lib/</environment_variable>
-                    <environment_variable name="FREETYPE_INCLUDE_DIR" action="set_to">$INSTALL_DIR/freetype/include/</environment_variable>
-                </action>
-            </actions>
-        </install>
-    </package>
-
 <package name="matplotlib" version="1.2.1">
         <install version="1.0">
             <actions>
                 <!-- first action is always downloading -->
                 <action type="download_by_url">http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.2.1/matplotlib-1.2.1.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="b7ff4a8c58df" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.7.1" />
+                    </repository>
+                    <repository changeset_revision="fe5cfaf931ff" name="package_freetype_2_4" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="freetype" version="2.4.11" />
+                    </repository>
+                </action>
 
                              
                 <!-- install matplotlib -->
@@ -85,7 +74,12 @@
  <package name="htseq" version="0.5.4">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p3.tar.gz</action>  
+                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p3.tar.gz</action> 
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="b7ff4a8c58df" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.7.1" />
+                    </repository>
+                </action>     
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;