From d71e3269e258a2a755799d40c9341479db6962a3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Manuel=20Dom=C3=ADnguez?=
 <dominguj@informatik.uni-freiburg.de>
Date: Tue, 5 Sep 2023 11:38:26 +0200
Subject: [PATCH 1/2] concat: Remove revision 855580142a12 from
 migrated_tools_conf.xml

Somebody disabled the tool renaming concat.xml to concat._xml. Revision 32e1c8dac438 is at the moment also installed, tagged with the same version number and working.
---
 files/galaxy/config/migrated_tools_conf.xml | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/files/galaxy/config/migrated_tools_conf.xml b/files/galaxy/config/migrated_tools_conf.xml
index 349f25340..89018e899 100644
--- a/files/galaxy/config/migrated_tools_conf.xml
+++ b/files/galaxy/config/migrated_tools_conf.xml
@@ -1043,17 +1043,6 @@
     </tool>
 </section>
 
-<section id="operate_on_genomic_intervals" name="Operate on Genomic Intervals" version="">
-  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/concat/855580142a12/concat/concat.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1">
-      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
-        <repository_name>concat</repository_name>
-        <repository_owner>devteam</repository_owner>
-        <installed_changeset_revision>855580142a12</installed_changeset_revision>
-        <id>toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1</id>
-        <version>1.0.1</version>
-    </tool>
-</section>
-
 <section id="gatk" name="GATK Tools" version="">
   <tool file="toolshed.g2.bx.psu.edu/repos/devteam/count_covariates/14e304b70425/count_covariates/count_covariates.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/count_covariates/gatk_count_covariates/0.0.5">
     <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>

From 03cfcc361b10ab71fbfd5de11cb30d25f5a40bf3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jos=C3=A9=20Manuel=20Dom=C3=ADnguez?=
 <dominguj@informatik.uni-freiburg.de>
Date: Tue, 5 Sep 2023 11:55:10 +0200
Subject: [PATCH 2/2] concat: Comment revision 855580142a12 from
 migrated_tools_conf.xml

Comment the tool revision instead of removing it.
---
 files/galaxy/config/migrated_tools_conf.xml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/files/galaxy/config/migrated_tools_conf.xml b/files/galaxy/config/migrated_tools_conf.xml
index 89018e899..f92ee0f3d 100644
--- a/files/galaxy/config/migrated_tools_conf.xml
+++ b/files/galaxy/config/migrated_tools_conf.xml
@@ -1043,6 +1043,17 @@
     </tool>
 </section>
 
+<!--section id="operate_on_genomic_intervals" name="Operate on Genomic Intervals" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/concat/855580142a12/concat/concat.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>concat</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>855580142a12</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1</id>
+        <version>1.0.1</version>
+    </tool>
+</section-->
+
 <section id="gatk" name="GATK Tools" version="">
   <tool file="toolshed.g2.bx.psu.edu/repos/devteam/count_covariates/14e304b70425/count_covariates/count_covariates.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/count_covariates/gatk_count_covariates/0.0.5">
     <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>