From d8af125af4d3798c32b31793c10f9b9426d7dfe2 Mon Sep 17 00:00:00 2001
From: Hans-Rudolf Hotz <hrhotz@users.noreply.github.com>
Date: Mon, 27 Mar 2017 17:08:17 +0200
Subject: [PATCH 1/3] Update __init__.py

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

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index e6d79f7ebab..3d4cfbbbea3 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -123,6 +123,7 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     "maf_by_block_number1",
     "wiggle2simple1",
     # Converters
+    "CONVERTER_bed_to_fli_0",
     "CONVERTER_fastq_to_fqtoc0",
     "CONVERTER_gff_to_interval_index_0",
     "CONVERTER_maf_to_fasta_0",

From 3068c9f053554c448a30388d46b91a6979e39cb7 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 27 Mar 2017 11:35:24 -0400
Subject: [PATCH 2/3] Fix CONVERTER_gff_to_fli_0 for striping Galaxy from
 Python environment.

Taking another stab at fixing #3499 which was broken with #3364. Last attempt at fixing converters didn't cover this (#3690) but I missed this tool and bed to fli fixed in #3822.
---
 lib/galaxy/tools/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 3d4cfbbbea3..325b1cbfa76 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -125,6 +125,7 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
     # Converters
     "CONVERTER_bed_to_fli_0",
     "CONVERTER_fastq_to_fqtoc0",
+    "CONVERTER_gff_to_fli_0",
     "CONVERTER_gff_to_interval_index_0",
     "CONVERTER_maf_to_fasta_0",
     "CONVERTER_maf_to_interval_0",

From 1fbdb35d6edb84a3700ea1392dcf32f1a42f8225 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Mon, 27 Mar 2017 17:44:40 -0400
Subject: [PATCH 3/3] Have IGV bigWig display application make use of
 build_sites/ site_type config instead of direct filename.

---
 display_applications/igv/bigwig.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/display_applications/igv/bigwig.xml b/display_applications/igv/bigwig.xml
index e8672262c97..5f5dc943111 100644
--- a/display_applications/igv/bigwig.xml
+++ b/display_applications/igv/bigwig.xml
@@ -2,7 +2,7 @@
 <display id="igv_bigwig" version="1.0.0" name="display with IGV">
     
     <!-- Load links from file: one line to one link -->
-    <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1">
+    <dynamic_links site_type="igv" skip_startswith="#" id="0" name="1">
         
         <!-- Define parameters by column from file, allow splitting on builds -->
         <dynamic_param name="site_id" value="0"/>