From 397d9609d78af602b2cbb788c71f8b9fb10315ab Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Mon, 9 Mar 2020 13:41:28 -0400
Subject: [PATCH 1/2] fix for python3 and GEDA, was getting "Connection closed
 at byte 0"

---
 lib/galaxy/webapps/galaxy/controllers/dataset.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index 708423f3a3b..10d1d26ee32 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -701,7 +701,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                                 else:
                                     file_name = value.file_name
                                 content_length = os.path.getsize(file_name)
-                                rval = open(file_name)
+                                rval = open(file_name, 'rb')
                             except OSError as e:
                                 log.debug("Unable to access requested file in display application: %s", e)
                                 return paste.httpexceptions.HTTPNotFound("This file is no longer available.")

From d0acfaf0a1384941fcc56dc41a9f2f2e9d702c7e Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan.blankenberg@gmail.com>
Date: Mon, 9 Mar 2020 13:53:14 -0400
Subject: [PATCH 2/2] fix for igv fasta having name=name=

---
 display_applications/igv/genome_fasta.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/display_applications/igv/genome_fasta.xml b/display_applications/igv/genome_fasta.xml
index 1dbb9d203e0..9f5295a3a35 100644
--- a/display_applications/igv/genome_fasta.xml
+++ b/display_applications/igv/genome_fasta.xml
@@ -70,10 +70,10 @@
 </jnlp>
 ]]>
         </param>
-        <param type="data" name="fai_file" dataset="fasta_file" url="galaxy_${DATASET_HASH}.fasta.fai" format="fai" />
+        <param type="data" name="fai_file" dataset="fasta_file" url="galaxy_${DATASET_HASH}.${fasta_file.ext}.fai" format="fai" />
         <param type="template" name="redirect_url" strip="True" >
             #if $site_id.startswith( 'local_' )
-                ${site_link}?genome=${fasta_file.qp}&amp;merge=true&amp;name=name=${qp( ( $fasta_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+                ${site_link}?genome=${fasta_file.qp}&amp;merge=true&amp;name=${qp( ( $fasta_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #elif $site_id.startswith( 'web_link_' ):
 ${site_link}?sessionURL=${fasta_file.qp}&amp;genome=${fasta_file.qp}&amp;merge=true&amp;name=${qp( ( $fasta_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
             #else: