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Commit 82a2374a authored by cyril.cros's avatar cyril.cros
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Prettier json

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.gitlab-ci.yml
+ 2
− 2
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......@@ -68,9 +68,9 @@ build_nginx_with_jbrowse_config_file:
# yamllint disable-line rule:line-length
- echo "{\"auths\":{\"$CI_REGISTRY\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /kaniko/.docker/config.json
script:
- echo "JBROWSE2_BASE='$CI_REGISTRY_IMAGE:jbrowse2-base-$CI_COMMIT_SHORT_SHA'"
- echo "IMG_BASE='$CI_REGISTRY_IMAGE:jbrowse2-base-$CI_COMMIT_SHORT_SHA'"
- /kaniko/executor --cache=true --context $CI_PROJECT_DIR/image
--build-arg "JBROWSE2_BASE='$CI_REGISTRY_IMAGE:jbrowse2-base-$CI_COMMIT_SHORT_SHA'"
--build-arg "IMG_BASE='$CI_REGISTRY_IMAGE:jbrowse2-base-$CI_COMMIT_SHORT_SHA'"
--dockerfile $CI_PROJECT_DIR/image/Dockerfile_advanced
--destination $CI_REGISTRY_IMAGE:jbrowse2-$CI_COMMIT_SHORT_SHA
- echo "Destination follows"
......
.pre-commit-config.yaml
+ 4
− 0
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......@@ -13,6 +13,10 @@ repos:
- id: end-of-file-fixer
- id: check-json
- id: check-yaml
args: [--allow-multiple-documents]
- id: double-quote-string-fixer
- id: pretty-format-json
args: [--autofix]
- repo: https://github.com/bridgecrewio/checkov.git
rev: 3.2.73
hooks:
......
.vscode/extensions.json
+ 8
− 8
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{
"recommendations": [
"ms-python.python",
"visualstudioexptteam.vscodeintellicode",
"tomoki1207.pdf",
"christian-kohler.path-intellisense",
"nextflow.nextflow",
"janisdd.vscode-edit-csv"
]
"recommendations": [
"ms-python.python",
"visualstudioexptteam.vscodeintellicode",
"tomoki1207.pdf",
"christian-kohler.path-intellisense",
"nextflow.nextflow",
"janisdd.vscode-edit-csv"
]
}
image/Dockerfile_advanced
+ 2
− 2
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# Stage 1: Jbrowse previous image
ARG JBROWSE2_BASE
FROM ${JBROWSE2_BASE} as jbrowse_builder
ARG IMG_BASE
FROM ${IMG_BASE} as jbrowse_builder
WORKDIR /app/annelids
COPY jbrowse_script_advanced.sh .
......
render_jbrowse2_config/config.json
+ 100
− 100
View file @ 82a2374a
{
"aggregateTextSearchAdapters": [
{
"assemblyNames": [
"pdumv021"
],
"ixFilePath": {
"locationType": "UriLocation",
"uri": "trix/pdumv021.ix"
},
"ixxFilePath": {
"locationType": "UriLocation",
"uri": "trix/pdumv021.ixx"
},
"metaFilePath": {
"locationType": "UriLocation",
"uri": "trix/pdumv021_meta.json"
},
"textSearchAdapterId": "pdumv021-index",
"type": "TrixTextSearchAdapter"
},
{
"assemblyNames": [
"pmassv1_masked"
],
"ixFilePath": {
"locationType": "UriLocation",
"uri": "trix/pmassv1_masked.ix"
},
"ixxFilePath": {
"locationType": "UriLocation",
"uri": "trix/pmassv1_masked.ixx"
},
"metaFilePath": {
"locationType": "UriLocation",
"uri": "trix/pmassv1_masked_meta.json"
},
"textSearchAdapterId": "pmassv1_masked-index",
"type": "TrixTextSearchAdapter"
}
],
"assemblies": [
{
"displayName": "Platynereis dumerilii genome v2.1 (pdumv021)",
"name": "pdumv021",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "pdumv021-ReferenceSequenceTrack",
"adapter": {
"type": "BgzipFastaAdapter",
"fastaLocation": {
"uri": "https://s3.embl.de/annelids/pdumv021/pdumv021.fa.gz",
"locationType": "UriLocation"
},
"faiLocation": {
"uri": "https://s3.embl.de/annelids/pdumv021/pdumv021.fa.gz.fai",
"locationType": "UriLocation"
"locationType": "UriLocation",
"uri": "https://s3.embl.de/annelids/pdumv021/pdumv021.fa.gz.fai"
},
"fastaLocation": {
"locationType": "UriLocation",
"uri": "https://s3.embl.de/annelids/pdumv021/pdumv021.fa.gz"
},
"gziLocation": {
"uri": "https://s3.embl.de/annelids/pdumv021/pdumv021.fa.gz.gzi",
"locationType": "UriLocation"
}
}
},
"displayName": "Platynereis dumerilii genome v2.1 (pdumv021)"
"locationType": "UriLocation",
"uri": "https://s3.embl.de/annelids/pdumv021/pdumv021.fa.gz.gzi"
},
"type": "BgzipFastaAdapter"
},
"trackId": "pdumv021-ReferenceSequenceTrack",
"type": "ReferenceSequenceTrack"
}
},
{
"displayName": "Platynereis massiliensis genome v1 - masked (pmassv1)",
"name": "pmassv1_masked",
"sequence": {
"type": "ReferenceSequenceTrack",
"trackId": "pmassv1_masked-ReferenceSequenceTrack",
"adapter": {
"type": "BgzipFastaAdapter",
"fastaLocation": {
"uri": "https://s3.embl.de/annelids/pmassv1_masked/pmassv1_masked.fa.gz",
"locationType": "UriLocation"
},
"faiLocation": {
"uri": "https://s3.embl.de/annelids/pmassv1_masked/pmassv1_masked.fa.gz.fai",
"locationType": "UriLocation"
"locationType": "UriLocation",
"uri": "https://s3.embl.de/annelids/pmassv1_masked/pmassv1_masked.fa.gz.fai"
},
"fastaLocation": {
"locationType": "UriLocation",
"uri": "https://s3.embl.de/annelids/pmassv1_masked/pmassv1_masked.fa.gz"
},
"gziLocation": {
"uri": "https://s3.embl.de/annelids/pmassv1_masked/pmassv1_masked.fa.gz.gzi",
"locationType": "UriLocation"
}
}
},
"displayName": "Platynereis massiliensis genome v1 - masked (pmassv1)"
"locationType": "UriLocation",
"uri": "https://s3.embl.de/annelids/pmassv1_masked/pmassv1_masked.fa.gz.gzi"
},
"type": "BgzipFastaAdapter"
},
"trackId": "pmassv1_masked-ReferenceSequenceTrack",
"type": "ReferenceSequenceTrack"
}
}
],
"configuration": {},
......@@ -54,96 +94,56 @@
},
"tracks": [
{
"type": "FeatureTrack",
"trackId": "annotation",
"name": "Gene models",
"adapter": {
"type": "Gff3TabixAdapter",
"gffGzLocation": {
"uri": "https://s3.embl.de/annelids/pdumv021/Annotation/pdumv021_Annotation_annotation.gff.gz",
"locationType": "UriLocation"
"locationType": "UriLocation",
"uri": "https://s3.embl.de/annelids/pdumv021/Annotation/pdumv021_Annotation_annotation.gff.gz"
},
"index": {
"indexType": "TBI",
"location": {
"uri": "https://s3.embl.de/annelids/pdumv021/Annotation/pdumv021_Annotation_annotation.gff.gz.tbi",
"locationType": "UriLocation"
},
"indexType": "TBI"
}
"locationType": "UriLocation",
"uri": "https://s3.embl.de/annelids/pdumv021/Annotation/pdumv021_Annotation_annotation.gff.gz.tbi"
}
},
"type": "Gff3TabixAdapter"
},
"category": [
"Annotation"
],
"assemblyNames": [
"pdumv021"
],
"description": "Kevin's GTF file"
"category": [
"Annotation"
],
"description": "Kevin's GTF file",
"name": "Gene models",
"trackId": "annotation",
"type": "FeatureTrack"
},
{
"type": "FeatureTrack",
"trackId": "annotation-pmass",
"name": "Gene models",
"adapter": {
"type": "Gff3TabixAdapter",
"gffGzLocation": {
"uri": "https://s3.embl.de/annelids/pmassv1_masked/Annotation/pmassv1_masked_Annotation_annotation.gff.gz",
"locationType": "UriLocation"
"locationType": "UriLocation",
"uri": "https://s3.embl.de/annelids/pmassv1_masked/Annotation/pmassv1_masked_Annotation_annotation.gff.gz"
},
"index": {
"indexType": "TBI",
"location": {
"uri": "https://s3.embl.de/annelids/pmassv1_masked/Annotation/pmassv1_masked_Annotation_annotation.gff.gz.tbi",
"locationType": "UriLocation"
},
"indexType": "TBI"
}
"locationType": "UriLocation",
"uri": "https://s3.embl.de/annelids/pmassv1_masked/Annotation/pmassv1_masked_Annotation_annotation.gff.gz.tbi"
}
},
"type": "Gff3TabixAdapter"
},
"category": [
"Annotation"
],
"assemblyNames": [
"pmassv1_masked"
],
"description": "Kevin's GTF file"
}
],
"aggregateTextSearchAdapters": [
{
"type": "TrixTextSearchAdapter",
"textSearchAdapterId": "pdumv021-index",
"ixFilePath": {
"uri": "trix/pdumv021.ix",
"locationType": "UriLocation"
},
"ixxFilePath": {
"uri": "trix/pdumv021.ixx",
"locationType": "UriLocation"
},
"metaFilePath": {
"uri": "trix/pdumv021_meta.json",
"locationType": "UriLocation"
},
"assemblyNames": [
"pdumv021"
]
},
{
"type": "TrixTextSearchAdapter",
"textSearchAdapterId": "pmassv1_masked-index",
"ixFilePath": {
"uri": "trix/pmassv1_masked.ix",
"locationType": "UriLocation"
},
"ixxFilePath": {
"uri": "trix/pmassv1_masked.ixx",
"locationType": "UriLocation"
},
"metaFilePath": {
"uri": "trix/pmassv1_masked_meta.json",
"locationType": "UriLocation"
},
"assemblyNames": [
"pmassv1_masked"
]
"category": [
"Annotation"
],
"description": "Kevin's GTF file",
"name": "Gene models",
"trackId": "annotation-pmass",
"type": "FeatureTrack"
}
]
}
render_jbrowse2_config/config_advanced.json
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This diff is collapsed.
render_jbrowse2_config/default_session.json
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{
"id": "34yhSDs6WtXGkpbAua9aZ",
"name": "Default pdumv021 view",
"views": [
{
"id": "nXdXs3K2UR6D6gxy8mp0I",
"minimized": false,
"type": "LinearGenomeView",
"offsetPx": 25940,
"bpPerPx": 34.36210526315789,
"displayedRegions": [
{
"reversed": false,
"refName": "scaffold_34",
"start": 0,
"end": 4679375,
"assemblyName": "pdumv021"
}
]
}
]
"id": "34yhSDs6WtXGkpbAua9aZ",
"name": "Default pdumv021 view",
"views": [
{
"bpPerPx": 34.36210526315789,
"displayedRegions": [
{
"assemblyName": "pdumv021",
"end": 4679375,
"refName": "scaffold_34",
"reversed": false,
"start": 0
}
],
"id": "nXdXs3K2UR6D6gxy8mp0I",
"minimized": false,
"offsetPx": 25940,
"type": "LinearGenomeView"
}
]
}
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