From ae1d7da3c5b924c66898c022dd0c6b380cae03d9 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 5 Aug 2013 23:50:04 -0500
Subject: [PATCH 1/4] Fix tool.requires_login behvaior broken with dynamic tool
 box filters (sorry again Dan and thanks for the bug report).

---
 lib/galaxy/tools/filters/__init__.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tools/filters/__init__.py b/lib/galaxy/tools/filters/__init__.py
index a99a94d7454..11b62334784 100644
--- a/lib/galaxy/tools/filters/__init__.py
+++ b/lib/galaxy/tools/filters/__init__.py
@@ -25,8 +25,7 @@ class FilterFactory( object ):
         """
         filters = self.default_filters.copy()
 
-        if not trans.user:
-            filters[ "tool" ].append( _requires_login )
+        filters[ "tool" ].append( _handle_requires_login )
 
         if kwds.get( "trackster", False ):
             filters[ "tool" ].append( _has_trackster_conf )
@@ -59,8 +58,8 @@ def _not_hidden( context, tool ):
     return not tool.hidden
 
 
-def _requires_login( context, tool ):
-    return not tool.require_login
+def _handle_requires_login( context, tool ):
+    return not tool.require_login or context.trans.user
 
 
 def _has_trackster_conf( context, tool ):

From 0dd2f9a5e09dd58b0aae183a01722fd77ae6e59b Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 6 Aug 2013 00:01:44 -0500
Subject: [PATCH 2/4] Slight simplification of logic related to implementation
 of tool.requires_login.

---
 lib/galaxy/tools/filters/__init__.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/lib/galaxy/tools/filters/__init__.py b/lib/galaxy/tools/filters/__init__.py
index 11b62334784..13bf9dc6435 100644
--- a/lib/galaxy/tools/filters/__init__.py
+++ b/lib/galaxy/tools/filters/__init__.py
@@ -12,7 +12,7 @@ class FilterFactory( object ):
         # Prepopulate dict containing filters that are always checked,
         # other filters that get checked depending on context (e.g. coming from
         # trackster or no user found are added in build filters).
-        self.default_filters = dict( tool=[ _not_hidden ], section=[], label=[] )
+        self.default_filters = dict( tool=[ _not_hidden, _handle_requires_login ], section=[], label=[] )
         # Add dynamic filters to these default filters.
         config = toolbox.app.config
         self.__init_filters( "tool", config.tool_filters )
@@ -25,8 +25,6 @@ class FilterFactory( object ):
         """
         filters = self.default_filters.copy()
 
-        filters[ "tool" ].append( _handle_requires_login )
-
         if kwds.get( "trackster", False ):
             filters[ "tool" ].append( _has_trackster_conf )
 

From 1cfcf5bc1ac58c90b43ec82cf826cd37b128d16c Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 6 Aug 2013 10:59:43 -0400
Subject: [PATCH 3/4] Add requirements tags to tophat wrapper.

---
 tools/ngs_rna/tophat_wrapper.xml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tools/ngs_rna/tophat_wrapper.xml b/tools/ngs_rna/tophat_wrapper.xml
index 56fdf30e359..a8961fe98a4 100644
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -3,6 +3,8 @@
     <description>Find splice junctions using RNA-seq data</description>
     <version_command>tophat --version</version_command>
     <requirements>
+        <requirement type="package">samtools</requirement>
+        <requirement type="package">bowtie</requirement>
         <requirement type="package">tophat</requirement>
     </requirements>
     <command interpreter="python">

From 20196a6e198ece6d74afa6ebd27ab26f4193fa92 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Tue, 6 Aug 2013 11:01:31 -0400
Subject: [PATCH 4/4] Add tophat2 to main tool conf.

---
 tool_conf.xml.main | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index aaf29cac3bc..cd4d0533a98 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -326,6 +326,7 @@
   <section name="NGS: RNA Analysis" id="ngs-rna-tools">
    <label text="RNA-seq" id="rna_seq" />
       <tool file="ngs_rna/tophat_wrapper.xml" />
+      <tool file="ngs_rna/tophat2_wrapper.xml" />
       <tool file="ngs_rna/cufflinks_wrapper.xml" />
       <tool file="ngs_rna/cuffcompare_wrapper.xml" />
  	    <tool file="ngs_rna/cuffmerge_wrapper.xml" />