From 182fbd1bc61f8ff8bd2cf29c23fca47c8eac7002 Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Tue, 19 May 2015 16:53:25 -0400
Subject: [PATCH 1/4] fix the data source tools for modendcode with proper URLs

---
 tools/data_source/fly_modencode.xml  | 2 +-
 tools/data_source/worm_modencode.xml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/data_source/fly_modencode.xml b/tools/data_source/fly_modencode.xml
index 7b14302ebec..70e080eec48 100644
--- a/tools/data_source/fly_modencode.xml
+++ b/tools/data_source/fly_modencode.xml
@@ -2,7 +2,7 @@
 <tool name="modENCODE fly" id="modENCODEfly" tool_type="data_source" version="1.0.0">
     <description>server</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
-    <inputs action="http://modencode.oicr.on.ca/fgb2/gbrowse/fly" check_values="false" target="_top"> 
+    <inputs action="http://gbrowse.modencode.org/fgb2/gbrowse/fly" check_values="false" target="_top"> 
         <display>go to modENCODE fly server $GALAXY_URL</display>
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEfly" />
     </inputs>
diff --git a/tools/data_source/worm_modencode.xml b/tools/data_source/worm_modencode.xml
index 074792cccf7..b2ade3a0e51 100644
--- a/tools/data_source/worm_modencode.xml
+++ b/tools/data_source/worm_modencode.xml
@@ -2,7 +2,7 @@
 <tool name="modENCODE worm" id="modENCODEworm" tool_type="data_source" version="1.0.0">
     <description>server</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
-    <inputs action="http://modencode.oicr.on.ca/fgb2/gbrowse/worm" check_values="false" target="_top"> 
+    <inputs action="http://gbrowse.modencode.org/fgb2/gbrowse/worm" check_values="false" target="_top"> 
         <display>go to modENCODE worm server $GALAXY_URL</display>
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEworm" />
     </inputs>

From 93c51fa25986d0cc2c0939879fc9e29e5e82568a Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <blankenberg@users.noreply.github.com>
Date: Wed, 20 May 2015 12:39:59 -0400
Subject: [PATCH 2/4] Update default dbkey for fly_modencode.xml and bump
 version.

dm3 is UCSC for release 5
---
 tools/data_source/fly_modencode.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/data_source/fly_modencode.xml b/tools/data_source/fly_modencode.xml
index 70e080eec48..3d3f5b8e533 100644
--- a/tools/data_source/fly_modencode.xml
+++ b/tools/data_source/fly_modencode.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool name="modENCODE fly" id="modENCODEfly" tool_type="data_source" version="1.0.0">
+<tool name="modENCODE fly" id="modENCODEfly" tool_type="data_source" version="1.0.1">
     <description>server</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
     <inputs action="http://gbrowse.modencode.org/fgb2/gbrowse/fly" check_values="false" target="_top"> 
@@ -7,15 +7,15 @@
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEfly" />
     </inputs>
     <request_param_translation>
-        <request_param galaxy_name="dbkey" remote_name="dbkey" missing="dm2" >
+        <request_param galaxy_name="dbkey" remote_name="dbkey" missing="dm3" >
             <value_translation>
-                <value galaxy_value="dm2" remote_value="fly" />
+                <value galaxy_value="dm3" remote_value="fly" />
             </value_translation>
         </request_param>
         <request_param galaxy_name="URL" remote_name="URL" missing="">
             <append_param separator="&amp;" first_separator="?" join="=">
                 <value name="d" missing="" />
-                <value name="dbkey" missing="dm2" />
+                <value name="dbkey" missing="dm3" />
                 <value name="q" missing="" />
                 <value name="s" missing="" />
                 <value name="t" missing="" />

From af6172d14d343e2e53fb757c93bbbab03edbfc6b Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <blankenberg@users.noreply.github.com>
Date: Wed, 20 May 2015 12:42:05 -0400
Subject: [PATCH 3/4] Update default dbkey for worm_modencode.xml and bump
 version.

ce10 is UCSC for WS220
---
 tools/data_source/worm_modencode.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/data_source/worm_modencode.xml b/tools/data_source/worm_modencode.xml
index b2ade3a0e51..b021f4a0ddf 100644
--- a/tools/data_source/worm_modencode.xml
+++ b/tools/data_source/worm_modencode.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool name="modENCODE worm" id="modENCODEworm" tool_type="data_source" version="1.0.0">
+<tool name="modENCODE worm" id="modENCODEworm" tool_type="data_source" version="1.0.1">
     <description>server</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
     <inputs action="http://gbrowse.modencode.org/fgb2/gbrowse/worm" check_values="false" target="_top"> 
@@ -7,15 +7,15 @@
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEworm" />
     </inputs>
     <request_param_translation>
-        <request_param galaxy_name="dbkey" remote_name="dbkey" missing="ce6" >
+        <request_param galaxy_name="dbkey" remote_name="dbkey" missing="ce10" >
             <value_translation>
-                <value galaxy_value="ce6" remote_value="worm" />
+                <value galaxy_value="ce10" remote_value="worm" />
             </value_translation>
         </request_param>
         <request_param galaxy_name="URL" remote_name="URL" missing="">
             <append_param separator="&amp;" first_separator="?" join="=">
                 <value name="d" missing="" />
-                <value name="dbkey" missing="ce6" />
+                <value name="dbkey" missing="ce10" />
                 <value name="q" missing="" />
                 <value name="s" missing="" />
                 <value name="t" missing="" />

From 8d2f9f77ebbdd4d2134fcd55304bb4aa1313f10b Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <blankenberg@users.noreply.github.com>
Date: Wed, 20 May 2015 12:47:01 -0400
Subject: [PATCH 4/4] Update modencode dbkeys in gbrowse_build_sites.txt

---
 tool-data/shared/gbrowse/gbrowse_build_sites.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tool-data/shared/gbrowse/gbrowse_build_sites.txt b/tool-data/shared/gbrowse/gbrowse_build_sites.txt
index 289af693b69..df21421f090 100644
--- a/tool-data/shared/gbrowse/gbrowse_build_sites.txt
+++ b/tool-data/shared/gbrowse/gbrowse_build_sites.txt
@@ -18,7 +18,7 @@ wormbase_ws225	WormBase WS225	http://ws225.wormbase.org/db/gb2/gbrowse/	caeAng1,
 tair	tair	http://arabidopsis.org/cgi-bin/gbrowse/	arabidopsis_tair8,arabidopsis,Arabidopsis_thaliana_TAIR10	arabidopsis_tair8,arabidopsis_tair9,arabidopsis
 
 #modENCODE
-modencode	modENCODE	http://modencode.oicr.on.ca/fgb2/gbrowse/	ce6,dm2	worm,fly
+modencode	modENCODE	http://gbrowse.modencode.org/fgb2/gbrowse/	ce10,dm3	worm,fly
 
 #Saccharomyces Genome Database (SGD)
 sgd_yeast	Saccharomyces Genome Database	http://browse.yeastgenome.org/fgb2/gbrowse/	Saccharomyces_cerevisiae_S288C_SGD2010	scgenome