# HG changeset patch
# User wolma
# Date 1461918006 14400
# Node ID 87b8dcebce9b5d0be1d04483b0ad96e0b5d5d9f8
# Parent  50ffd429060b9f0ea1a02047129789bf58002c46
Uploaded

diff -r 50ffd429060b -r 87b8dcebce9b tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 26 12:24:47 2016 -0400
+++ b/tool_dependencies.xml	Fri Apr 29 04:20:06 2016 -0400
@@ -5,25 +5,24 @@
   </package>
   
   <package name="sqlite" version="3.8.3">
-    <repository changeset_revision="706b1f3b1fc0" name="package_sqlite_3_8_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="c8a5c11cc921" name="package_sqlite_3_8_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   
   <package name="python3" version="3.4">
-      <install version="1.0">
-          <actions>
-              <action type="download_by_url">https://www.python.org/ftp/python/3.4.4/Python-3.4.4.tgz</action>
-              
-                <action type="set_environment_for_install">
-                  <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                      <package name="zlib" version="1.2.8" />
-                  </repository>
-                    
-                  <repository changeset_revision="706b1f3b1fc0" name="package_sqlite_3_8_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
-                    <package name="sqlite" version="3.8.3" />
-                  </repository>
-                </action>
-                
-                <action type="shell_command">
+    <install version="1.0">
+      <actions>
+        <action type="download_by_url">https://www.python.org/ftp/python/3.4.4/Python-3.4.4.tgz</action>
+
+        <action type="set_environment_for_install">
+          <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+            <package name="zlib" version="1.2.8" />
+          </repository>
+          <repository changeset_revision="c8a5c11cc921" name="package_sqlite_3_8_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+            <package name="sqlite" version="3.8.3" />
+          </repository>
+        </action>
+
+        <action type="shell_command">
           # The python build system doesn't check CPATH / C(PLUS)_INCLUDE_PATH which is set by the depended-upon
           # tool definitions for these sources, but it does check CPPFLAGS / LDFLAGS
           # Currently not whitespace-safe, I haven't found a way yet to quote the *FLAGS values so that they are
@@ -47,24 +46,24 @@
           unset PYTHONPATH
           unset PYTHONHOME
 
-          ./configure --prefix="$INSTALL_DIR" \
+          ./configure --prefix="$INSTALL_DIR" --without-ensurepip \
           &amp;&amp; make \
           &amp;&amp; make install
-                </action>
-                
-                <action type="set_environment">
-                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
-                    <!-- clear PYTHONPATH, otherwise we will get Galaxy's Python 2 libraries in the Python 3 path. -->
-                    <environment_variable action="set_to" name="PYTHONPATH" />
-                    <environment_variable action="set_to" name="PYTHONHOME">$INSTALL_DIR</environment_variable>
-                    <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable>
-                    <!-- fix too strict compiler settings under Python 3.4 -->
-                    <environment_variable action="set_to" name="CFLAGS">"$ENV[CFLAGS] -Wno-error=declaration-after-statement"</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
+        </action>
+
+        <action type="set_environment">
+          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+          <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[ZLIB_ROOT_PATH]/lib</environment_variable>
+          <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[SQLITE_ROOT_DIR]/lib</environment_variable>
+          <!-- clear PYTHONPATH, otherwise we will get Galaxy's Python 2 libraries in the Python 3 path. -->
+          <environment_variable action="set_to" name="PYTHONPATH" />
+          <environment_variable action="set_to" name="PYTHONHOME">$INSTALL_DIR</environment_variable>
+          <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable>
+        </action>
+      </actions>
+    </install>
+    
+    <readme>
       The Python programming language version 3.4
 
       http://www.python.org
@@ -74,9 +73,9 @@
       
       This package receives bug fixes within the 3.4 release series!
       
-      It contains the zlib and sqlite3 modules as the only stdlib modules with 
-      external dependencies (handled in here by depending on package_zlib_1_2_8 
-      and package_sqlite_3_8_3). 
+      Currently, it contains the zlib and sqlite3 modules as the only stdlib 
+      modules with external dependencies (handled in here by depending on 
+      package_zlib_1_2_8 and package_sqlite_3_8_3). 
       
       In particular, this build does not compile Python's ssl module (which 
       would cause dependency on openssl and, in turn, on Perl).
@@ -84,16 +83,16 @@
       This means that **the pip installation tool will not be available with 
       this build** !! 
       
-      For a full build (including the ssl module) look at 
-      https://toolshed.g2.bx.psu.edu/view/jankanis/package_python3_4 
-      written by jankanis, of which this package is a shameless plagiarism. 
+      For a full build (including the ssl module) look at
+      https://toolshed.g2.bx.psu.edu/view/iuc/package_python_3_4/
+      issued by the IUC. 
 
       This version of Python includes a built-in virtual environment manager. 
       To create a Python 3 virtual env, include the following actions in your 
       tool_dependencies.xml, e.g. for a package MY_TOOL_venv:
 
       &lt;action type="set_environment_for_install"&gt;
-        &lt;repository name="package_python3_zlib_dependent_1_0" owner="wolma"&gt;
+        &lt;repository name="package_python_3_4_x_lean" owner="wolma"&gt;
           &lt;package name="python3" version="3.4" /&gt;
         &lt;/repository&gt;
         &lt;!-- other install time dependencies --&gt;
@@ -105,7 +104,9 @@
         # pip cannot be used for installation because it depends on ssl, 
         # which this build does not provide
         
-        pyvenv --without-pip $INSTALL_DIR/MY_TOOL_venv
+        python3 -m venv --without-pip $INSTALL_DIR/MY_TOOL_venv
+        
+        # optional: install setuptools if required
         
         # install python packages
         # assuming you are in the download directory of the package
@@ -113,10 +114,9 @@
         $INSTALL_DIR/MY_TOOL_venv/bin/python3 setup.py install 
       &lt;/action&gt;
       
-    For an example of how this could used by a package look at the 
-    tool_dependencies file of:
+    For a full example look at the tool_dependencies file of:
     
-    https://toolshed.g2.bx.psu.edu/view/wolma/mimodd
+        https://toolshed.g2.bx.psu.edu/view/wolma/mimodd
     
     </readme>
   </package>