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Commit 54cb7437 authored by cyril.cros's avatar cyril.cros
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Editing rules and image

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.gitlab-ci.yml
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......@@ -45,14 +45,18 @@ build_nginx_with_jbrowse_config_file:
--dockerfile $CI_PROJECT_DIR/image/Dockerfile
--destination $CI_REGISTRY_IMAGE:jbrowse2-$CI_COMMIT_SHORT_SHA
- echo "Uploaded to $CI_REGISTRY_IMAGE:jbrowse2-$CI_COMMIT_SHORT_SHA"
rules:
- changes:
- image/**/*
deploy_to_k8s:
stage: deploy
image: dtzar/helm-kubectl:3.8.2
needs:
- cluster_access_test
- s3_access_test
- build_nginx_with_jbrowse_config_file
- name: cluster_access_test
- name: s3_access_test
- name: build_nginx_with_jbrowse_config_file
optional: true
before_script:
- echo $KUBECONFIG | base64 -d > /tmp/kubeconf
- export KUBECONFIG=/tmp/kubeconf
......
TODO.md
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......@@ -3,3 +3,4 @@
- check if CORS has issues
- add anoter script tag <script> window.__jbrowseCacheBuster = true </script> within <head></head>
- check if the default session does work
- URL config: https://genomes-testing.arendt.embl.de/?assembly=pdumv021&loc=scaffold_34:855,274..944,843&tracklist=true&tracks=pdumv021-ReferenceSequenceTrack,pdumv021-annotation
image/jbrowse_script_base.sh
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......@@ -6,6 +6,6 @@ jbrowse add-assembly https://s3.embl.de/annelids/pdumv021/pdumv021.fa.gz -n "pdu
jbrowse add-assembly https://s3.embl.de/annelids/pmassv1_masked/pmassv1_masked.fa.gz -n "pmassv1_masked" --displayName "Platynereis massiliensis genome v1 - masked (pmassv1)" --gziLocation https://s3.embl.de/annelids/pmassv1_masked/pmassv1_masked.fa.gz.gzi --faiLocation https://s3.embl.de/annelids/pmassv1_masked/pmassv1_masked.fa.gz.fai -t bgzipFasta
# Reference annotation
jbrowse add-track https://s3.embl.de/annelids/pdumv021/Annotation/pdumv021_Annotation_annotation.gff.gz -a "pdumv021" -d "Kevin's GTF file" -n "Gene models" --category "Annotation" --trackId "annotation" --indexFile https://s3.embl.de/annelids/pdumv021/Annotation/pdumv021_Annotation_annotation.gff.gz.tbi
jbrowse add-track https://s3.embl.de/annelids/pmassv1_masked/Annotation/pmassv1_masked_Annotation_annotation.gff.gz -a "pmassv1_masked" -d "Kevin's GTF file" -n "Gene models" --category "Annotation" --trackId "annotation-pmass" --indexFile https://s3.embl.de/annelids/pmassv1_masked/Annotation/pmassv1_masked_Annotation_annotation.gff.gz.tbi
jbrowse add-track https://s3.embl.de/annelids/pmassv1_masked/Annotation/pmassv1_masked_Annotation_annotation.gff.gz -a "pmassv1_masked" -d "Kevin's GTF file" -n "Gene models" --category "Annotation" --trackId "annotation" --indexFile https://s3.embl.de/annelids/pmassv1_masked/Annotation/pmassv1_masked_Annotation_annotation.gff.gz.tbi
# Text index
jbrowse text-index
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