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Merge pull request #9653 from mvdbeek/igv_vcf_display_application_enhancements_and_fixes

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[20.01] Fix vcf_bgzip mimetype, allow cors, tbi from metadata element
This commit is contained in:
Dannon
2020-04-24 12:52:56 -04:00
committed by GitHub
parent 9397576e4e 58c82ad7f3
commit a07a50fff8
2 changed files with 10 additions and 5 deletions
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.github/workflows/integration.yaml
+6 -1
View File
@@ -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 ${{ steps.minikube.outputs.launcher }}
display_applications/igv/vcf.xml
+4 -4
View File
@@ -12,8 +12,8 @@
<filter>${$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 -->