From 6af1eb0eb7ca4824a2ab7d4d58cddf0c5fb0d524 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 17 Sep 2014 10:27:56 +0000
Subject: [PATCH 1/3] Add $INSTALL_DIR to PERL5LIB and PATH before starting to
 install libraries. A few packages need this in order to recognise previous
 installed packages.

---
 .../galaxy_install/tool_dependencies/recipe/step_handler.py     | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
index 6d64e9c96a0..e1ca6e59a2f 100644
--- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
+++ b/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

From 4a17892400883d4f8c354bfa47ff51700e115603 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 22 Sep 2014 11:23:02 -0400
Subject: [PATCH 2/3] Always access EBI SRA via HTTPS.

Thanks to Ilya for opening pull request to make it conditionally use HTTPS - https://bitbucket.org/galaxy/galaxy-central/pull-request/491/remove-http-from-ebi-url-which-is/diff - but this goes one step further and always uses HTTPS as suggested by Nate in the pull request comments.
---
 tools/data_source/ebi_sra.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/data_source/ebi_sra.xml b/tools/data_source/ebi_sra.xml
index 8d49a2e4dad..8336c87453c 100644
--- a/tools/data_source/ebi_sra.xml
+++ b/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"/>

From e56943de8ca4a3acef43172f69272c4372843045 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Mon, 22 Sep 2014 11:31:56 -0400
Subject: [PATCH 3/3] Always access UCSC Main via HTTPS.

---
 tools/data_source/ucsc_tablebrowser.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/data_source/ucsc_tablebrowser.xml b/tools/data_source/ucsc_tablebrowser.xml
index 3a7154e23cc..fcf1d92c4e7 100644
--- a/tools/data_source/ucsc_tablebrowser.xml
+++ b/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" />