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Arendt Group
Jbrowse2 Annelids
Commits
54cb7437
Commit
54cb7437
authored
5 months ago
by
cyril.cros
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Editing rules and image
parent
b9da7ce7
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Pipeline
#65924
failed
5 months ago
Changes
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3 changed files
.gitlab-ci.yml
+7
-3
7 additions, 3 deletions
.gitlab-ci.yml
TODO.md
+1
-0
1 addition, 0 deletions
TODO.md
image/jbrowse_script_base.sh
+1
-1
1 addition, 1 deletion
image/jbrowse_script_base.sh
with
9 additions
and
4 deletions
.gitlab-ci.yml
+
7
−
3
View file @
54cb7437
...
...
@@ -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
...
...
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TODO.md
+
1
−
0
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54cb7437
...
...
@@ -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
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image/jbrowse_script_base.sh
+
1
−
1
View file @
54cb7437
...
...
@@ -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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