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Commit 5fff2ac2 authored by Cyril Christophe Daniel Robert Cros's avatar Cyril Christophe Daniel Robert Cros
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Merge branch 'pre-commit' into 'main'

Pre-commit

See merge request !2
parents caf32893 389c1252
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1 merge request!2Pre-commit
Pipeline #58402 passed
tmp/*
\ No newline at end of file
tmp/*
......@@ -14,8 +14,8 @@ s3_access_test:
image: minio/mc
stage: access_test
rules:
- changes: # TODO change where necessary
- image/*
- changes: # TODO change where necessary
- image/*
before_script:
- mc alias set genomes $S3_ENDPOINT $S3_ACCESS_KEY $S3_SECRET_KEY
script:
......@@ -36,10 +36,11 @@ build_nginx_with_jbrowse_config_file:
image: gcr.io/kaniko-project/executor:debug-v0.21.0
stage: build_container
before_script:
# yamllint disable-line rule:line-length
- echo "{\"auths\":{\"$CI_REGISTRY\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /kaniko/.docker/config.json
script:
- /kaniko/executor --cache=true --context $CI_PROJECT_DIR/image
--dockerfile $CI_PROJECT_DIR/image/Dockerfile
- /kaniko/executor --cache=true --context $CI_PROJECT_DIR/image
--dockerfile $CI_PROJECT_DIR/image/Dockerfile
--destination $CI_REGISTRY_IMAGE:jbrowse2-$CI_COMMIT_SHORT_SHA
kustomize_build_apply:
......@@ -53,7 +54,8 @@ kustomize_build_apply:
- cat deployment/jbrowse2-dep.yaml
- kubectl apply -k deployment
- kubectl -n $NS rollout restart deployment/jbrowse2
- kubectl -n $NS wait --for=condition=available --timeout=60s deploy/jbrowse2
- kubectl -n $NS wait --for=condition=available
--timeout=60s deploy/jbrowse2
- kubectl -n $NS rollout status deployment/jbrowse2
dependencies:
- cluster_access_test
......
---
repos:
- repo: https://github.com/adrienverge/yamllint.git
rev: v1.35.1
hooks:
- id: yamllint
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.6.0
hooks:
- id: check-merge-conflict
- id: trailing-whitespace
- id: check-added-large-files
- id: end-of-file-fixer
- repo: https://github.com/bridgecrewio/checkov.git
rev: 3.2.73
hooks:
- id: checkov
args: [-d .]
- repo: https://github.com/Agilicus/pre-commit-hook-k8svalidate.git
rev: v0.2.0
hooks:
- id: k8svalidate
files: .yml$
- repo: https://github.com/Yelp/detect-secrets
rev: v1.4.0
hooks:
- id: detect-secrets
......@@ -4,6 +4,6 @@
"visualstudioexptteam.vscodeintellicode",
"tomoki1207.pdf",
"christian-kohler.path-intellisense",
"nextflow.nextflow"
"nextflow.nextflow"
]
}
......@@ -2,4 +2,4 @@
- use htslib for bgzip and tabix
- npx @jbrowse/cli add-assembly https://s3.embl.de/annelids/pdumv021_genome.fa.gz --name pdumv021
- use SAMtools for faidx
\ No newline at end of file
- use SAMtools for faidx
......@@ -17,7 +17,7 @@ spec:
app: jbrowse2
spec:
imagePullSecrets:
- name: gitlab-token-auth
- name: gitlab-token-auth
containers:
- name: jbrowse2
image: ${CI_REGISTRY_IMAGE}:jbrowse2-${CI_COMMIT_SHORT_SHA}
......@@ -28,7 +28,7 @@ spec:
cpu: 1
limits:
memory: 4096Mi
cpu: 2
cpu: 1
ports:
- name: http
containerPort: 80
......@@ -70,4 +70,4 @@ spec:
name: http
tls:
- hosts:
- ${JBROWSE_HOSTNAME}
\ No newline at end of file
- ${JBROWSE_HOSTNAME}
---
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
- jbrowse2-dep.yaml
- jbrowse2-dep.yaml
labels:
- includeSelectors: true
pairs:
app: jbrowse2
- includeSelectors: true
pairs:
app: jbrowse2
name,url
pdumv021,https://s3.embl.de/annelids/pdumv021/pdumv021_genome.fa.gz
\ No newline at end of file
pdumv021,https://s3.embl.de/annelids/pdumv021/pdumv021_genome.fa.gz
"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN035.vcf"
"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN054.vcf"
"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN054.vcf"
"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN055.vcf"
"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN056.vcf"
"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN057.vcf"
......@@ -17,4 +17,4 @@
"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN028.vcf"
"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN029.vcf"
"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN030.vcf"
"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN031.vcf"
\ No newline at end of file
"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN031.vcf"
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