Repository 'blast2html'
hg clone https://toolshed.g2.bx.psu.edu/repos/jankanis/blast2html

Changeset 87:62aac637dd6c (2014-06-24)
Previous changeset 86:463744384507 (2014-06-24) Next changeset 88:24deecb59ce9 (2014-06-24)
Commit message:
(attempt to) get lxml install working
modified:
tool_dependencies.xml
b
diff -r 463744384507 -r 62aac637dd6c tool_dependencies.xml
--- a/tool_dependencies.xml Tue Jun 24 11:20:24 2014 +0200
+++ b/tool_dependencies.xml Tue Jun 24 16:46:18 2014 +0200
[
@@ -25,16 +25,19 @@
         </action>
 
  <action type="setup_virtualenv">
-   lxml==3.3.5
    jinja2==2.7.3
    six==1.7.2
    argparse==1.2.1
  </action>
-        
+
+ <!-- install lxml manually, as the setup_virtualenv action does not include the environment
+      from set_environment_for_install but shell_command does -->
+ <action type="shell_command">
+   $INSTALL_DIR/venv/bin/pip install lxml==3.3.5
+ </action>
+
         <action type="set_environment">
-          <!-- To find shared libraries such as libssl or libxml2 -->
-          <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LD_LIBRARY_PATH]</environment_variable>
-          <!-- libxml2 doesn't actually export its own LD_LIBRARY_PATH -->
+          <!-- add libxml2 library path so the runtime can find the shared library -->
           <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LIBXML_ROOT_PATH]/lib</environment_variable>
         </action>
       </actions>