# HG changeset patch
# User wolma
# Date 1407933025 14400
# Node ID f16443335cbacb9593d5910fc8c4ccaf67ef326a
# Parent  ecf7415d602ca4538a2d6064a2f1fe6caa25d079
Deleted selected files

diff -r ecf7415d602c -r f16443335cba tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Aug 12 12:05:14 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,130 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="zlib" version="1.2.8">
-      <repository changeset_revision="9d017266c41e" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-  </package>
-  
-  <package name="python3" version="3.4.1">
-    <install version="1.0">
-      <actions>
-        <action type="download_by_url">https://www.python.org/ftp/python/3.4.1/Python-3.4.1.tgz</action>
-
-        <action type="set_environment_for_install">
-          <repository changeset_revision="9d017266c41e" name="package_zlib_1_2_8" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu">
-            <package name="zlib" version="1.2.8" />
-          </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
-          # correctly recognized by both the python build process and the compiler. But as galaxy itself isn't
-          # whitespace-safe either it doesn't really matter (currently).
-          oldifs="$IFS"
-          IFS=":"
-          for p in $CPLUS_INCLUDE_PATH
-          do
-              CPPFLAGS="$CPPFLAGS -I$p"
-          done
-          for p in $LD_LIBRARY_PATH
-          do
-              LDFLAGS="$LDFLAGS -L$p"
-          done
-          IFS="$oldifs"
-          export CPPFLAGS
-          export LDFLAGS
-
-          # Clear variables that may be used in Galaxy's extenal python 2 environment
-          unset PYTHONPATH
-          unset PYTHONHOME
-
-          ./configure --prefix="$INSTALL_DIR" --with-ensurepip \
-          &amp;&amp; make \
-          &amp;&amp; make install
-        </action>
-
-        <action type="set_environment">
-          <environment_variable action="prepend_to" name="PATH">$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>
-        </action>
-      </actions>
-    </install>
-
-    <readme>
-      Python 3.4.1
-
-      The Python programming language version 3.
-
-      http://www.python.org
-
-
-      A lean build of python 3.4.1. It does not include modules with external dependencies except for the zlib module, which requires the zlib library installed on your system. For a build with more such modules included look at https://toolshed.g2.bx.psu.edu/view/jankanis/package_python3_4 written by jankanis, of which this package is a shameless plagiarism. 
-
-      Python as of version 3.3 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="python3" owner="wolma"&gt;
-          &lt;package name="python3" version="3.4.1" /&gt;
-        &lt;/repository&gt;
-        &lt;!-- other install time dependencies --&gt;
-      &lt;/action&gt;
-
-      &lt;action type="shell_command"&gt;
-        # Unset any saved environment settings from parent virtual
-        # environments, e.g. for python 2 or if Galaxy itself is running
-        # from within a virtual environment.
-        unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME
-        # Create virtual environment MY_TOOL_venv
-        pyvenv MY_TOOL_venv
-        # install python packages
-        MY_TOOL_venv/bin/pip3 install {{NEEDED_PYTHON_PACKAGES}}
-      &lt;/action&gt;
-
-      &lt;action type="set_environment"&gt;
-
-	&lt;!-- Setting the PYTHONPATH correctly can be a bit tricky, because you must
-             make sure that the runtime PYTHONPATH from galaxy itself is not
-             included, as it probably points to python 2 code that can crash a
-             program if python 3 tries to load it.
-
-             If you only use a single virtual environment that is created
-             specifically for a tool you are creating, you can just use a set_to
-             like below.
-
-             If you create a virtual environment installation that is meant to be
-             reused by other packages, the virtual environment should probably
-             prepend its site-packages to the PYTHONPATH since a tool could be
-             using python modules from several virtual environments. But in such a
-             scenario the tool that uses these virtual environments should also
-             depend directly on the python3 package, and this dependency should be
-             listed before any virtual environment dependencies. This ensures that
-             the python3 environment settings that clear PYTHONPATH are sourced
-             first so galaxy's runtime PYTHONPATH is excluded. Virtual environments
-             can then prepend their PYTHONPATHs to each other. --&gt;
-        &lt;environment_variable name="PYTHONPATH" action="set_to"&gt;$INSTALL_DIR/MY_TOOL_venv/lib/python3.4/site-packages&lt;/environment_variable&gt;
-        &lt;!-- All that is really needed to use a specific virtual environment is that the
-             python interpreter in that environment is used, so add it to PATH --&gt;
-        &lt;environment_variable name="PATH" action="prepend_to"&gt;$INSTALL_DIR/MY_TOOL_venv/bin&lt;/environment_variable&gt;
-        &lt;!-- Clear incoming PYTHONHOME just like the venv's 'activate' command does --&gt;
-        &lt;environment_variable name="PYTHONHOME" action="set_to"&gt;&lt;/environment_variable&gt;
-        &lt;!-- To find shared libraries for python built-in modules such as libssl or libsqlite3
-             we need to re-export LD_LIBRARY_PATH --&gt;
-        &lt;environment_variable name="LD_LIBRARY_PATH" action="prepend_to"&gt;$ENV[LD_LIBRARY_PATH]&lt;/environment_variable&gt;
-      &lt;/action&gt;
-
-
-      Then, in your MY_TOOL.xml add the following requirement:
-
-      &lt;requirements&gt;
-        &lt;requirement name="package" version="XXX"&gt;MY_TOOL_venv&lt;/requirement&gt;
-      &lt;/requirements&gt;
-      
-    </readme>
-
-  </package>
-</tool_dependency>