From bf4fb7735970568d56bd427e208b084a92ad87cb Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 2 Apr 2020 19:53:59 +0200
Subject: [PATCH 1/2] Delete 15G dotnet folder, use minikube 1.9.0

---
 .github/workflows/integration.yaml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml
index 25edfff1b8c..fb3ff8d1648 100644
--- a/.github/workflows/integration.yaml
+++ b/.github/workflows/integration.yaml
@@ -27,10 +27,15 @@ jobs:
     steps:
     - name: Prune unused docker image, volumes and containers
       run: docker system prune -a -f
+    - name: Clean dotnet folder for space
+      if: matrix.subset == 'kubernetes'
+      run: rm -Rf /usr/share/dotnet
     - name: Setup Minikube
       if: matrix.subset == 'kubernetes'
       id: minikube
-      uses: CodingNagger/minikube-setup-action@v1.0.2
+      uses: CodingNagger/minikube-setup-action@v1.0.3
+      with:
+        minikube-version: "1.9.0-0_amd64"
     - name: Launch Minikube
       if: matrix.subset == 'kubernetes'
       run: eval ${{ steps.minikube.outputs.launcher }}

From 58c82ad7f37eb577ef66a0546415c76873064bc2 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 24 Apr 2020 13:19:56 +0200
Subject: [PATCH 2/2] Fix vcf_bgzip mimetype, allow cors, tbi from metadata
 element

The mimetype would be text/plain otherwise, which is not compatible with
byte-range requests. `allow_cors` doesn't quite seem to work in my
tests, but we'll need this for jbrowse.

Also skips an additional conversion by using the tabix index, which
again is helpful when loading datasets from a shared history.
---
 display_applications/igv/vcf.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/display_applications/igv/vcf.xml b/display_applications/igv/vcf.xml
index f2c1e07966a..3c66ffd677a 100644
--- a/display_applications/igv/vcf.xml
+++ b/display_applications/igv/vcf.xml
@@ -12,8 +12,8 @@
         <filter>${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
         <url>${redirect_url}</url>
-        <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
-        <param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
+        <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" allow_cors="true" mimetype="application/octet-stream"/>
+        <param type="data" name="tabix_file" metadata="tabix_index" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" allow_cors="true" mimetype="application/octet-stream"/>
         <param type="template" name="site_organism" strip="True" >
             #if ($dataset.dbkey in $site_dbkeys)
                 $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ]
@@ -94,8 +94,8 @@
         <filter>${ $dataset.dbkey == $value }</filter>
         <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
         <url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bgzip_file.qp}&amp;genome=${qp($bgzip_file.dbkey)}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
-        <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
-        <param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
+        <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" mimetype="application/octet-stream"/>
+        <param type="data" name="tabix_file" metadata="tabix_index" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="vcf_bgzip" mimetype="application/octet-stream"/>
     </dynamic_links>
 </display>
 <!-- Dan Blankenberg -->