From b98b3a14c3cb01fa5a366ec437d0ec2aa0bb7bae Mon Sep 17 00:00:00 2001
From: Rayane Elmedjadji <122781957+elmedjadjirayane@users.noreply.github.com>
Date: Fri, 23 May 2025 18:15:19 +0200
Subject: [PATCH 1/4] Add gwas_bgzip.

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 49270c49811..c9845961c4a 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -597,6 +597,7 @@
     <datatype extension="bed_tabix.gz" type="galaxy.datatypes.interval:BedTabix" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="gff_tabix.gz" type="galaxy.datatypes.interval:GffTabix" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="bgzip" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
+    <datatype extension="gwas_bgzip" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
     <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">
       <display file="igv/vcf.xml"/>
       <converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/>

From e5527454807aae4a13c64cb92a265a9266db385f Mon Sep 17 00:00:00 2001
From: Rayane Elmedjadji <122781957+elmedjadjirayane@users.noreply.github.com>
Date: Fri, 23 May 2025 18:25:28 +0200
Subject: [PATCH 2/4] Add gwas_tabix.gz datatype.

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index c9845961c4a..88c6883c61c 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -598,6 +598,7 @@
     <datatype extension="gff_tabix.gz" type="galaxy.datatypes.interval:GffTabix" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="bgzip" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
     <datatype extension="gwas_bgzip" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
+    <datatype extension="gwas_tabix.gz" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
     <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">
       <display file="igv/vcf.xml"/>
       <converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/>

From 1db5d5ca1b08b4fbea521c98ea95eecbe13cd434 Mon Sep 17 00:00:00 2001
From: Rayane Elmedjadji <122781957+elmedjadjirayane@users.noreply.github.com>
Date: Mon, 26 May 2025 14:02:43 +0200
Subject: [PATCH 3/4] Update datatypes_conf.xml.sample

---
 lib/galaxy/config/sample/datatypes_conf.xml.sample | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 88c6883c61c..8ac23cb2a1b 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -597,8 +597,10 @@
     <datatype extension="bed_tabix.gz" type="galaxy.datatypes.interval:BedTabix" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="gff_tabix.gz" type="galaxy.datatypes.interval:GffTabix" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="bgzip" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
+    <!-- GWAS results datatypes to be used with locuszoom visualization plugin -->
     <datatype extension="gwas_bgzip" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
     <datatype extension="gwas_tabix.gz" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
+    <!-- -->
     <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">
       <display file="igv/vcf.xml"/>
       <converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/>

From 249dcdbf3ed950dc585bbbcd601128a0fca2c2ad Mon Sep 17 00:00:00 2001
From: Rayane Elmedjadji <122781957+elmedjadjirayane@users.noreply.github.com>
Date: Mon, 26 May 2025 16:24:12 +0200
Subject: [PATCH 4/4] add locuszoom to visualizations.yml

---
 client/visualizations.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/client/visualizations.yml b/client/visualizations.yml
index 767c85c5ff1..61fa6b854f3 100644
--- a/client/visualizations.yml
+++ b/client/visualizations.yml
@@ -39,6 +39,9 @@ jupyterlite:
 kepler:
     package: "@galaxyproject/kepler"
     version: 0.0.3
+locuszoom:
+    package: "@galaxyproject/locuszoom"
+    version: 0.0.6
 molstar:
     package: "@galaxyproject/molstar"
     version: 0.0.2