Merge last minute bug fixes from default.

lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py

@@ -1105,6 +1105,8 @@ class SetupPerlEnvironment( Download, RecipeStep ):
                     # If set to a true value then MakeMaker's prompt function will always
                     # return the default without waiting for user input.
                     cmd = '''PERL_MM_USE_DEFAULT=1; export PERL_MM_USE_DEFAULT; '''
+                    cmd += 'export PERL5LIB=$INSTALL_DIR/lib/perl5:$PERL5LIB;'
+                    cmd += 'export PATH=$INSTALL_DIR/bin:$PATH;'
                     if perl_package.find( '://' ) != -1:
                         # We assume a URL to a gem file.
                         url = perl_package

tools/data_source/ebi_sra.xml

@@ -4,7 +4,7 @@
     <!-- This paython script imports the file into Galaxy -->
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
     <!-- The URL where Galaxy will forwards the user when this tool is accessed from the Get Data menu -->
-    <inputs action="http://www.ebi.ac.uk/ena/data/search" check_values="false" method="get">
+    <inputs action="https://www.ebi.ac.uk/ena/data/search" check_values="false" method="get">
         <display>go to EBI SRA server $GALAXY_URL</display>
     </inputs>
     <uihints minwidth="800"/>

tools/data_source/ucsc_tablebrowser.xml

@@ -7,7 +7,7 @@
 <tool name="UCSC Main" id="ucsc_table_direct1" tool_type="data_source">
     <description>table browser</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
-    <inputs action="http://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
+    <inputs action="https://genome.ucsc.edu/cgi-bin/hgTables" check_values="false" method="get">
         <display>go to UCSC Table Browser $GALAXY_URL</display>
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
         <param name="tool_id" type="hidden" value="ucsc_table_direct1" />