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Commit e2a25fb6 authored by Cyril Christophe Daniel Robert Cros's avatar Cyril Christophe Daniel Robert Cros
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Nextflow work

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1 merge request!6Nextflow work
......@@ -2,8 +2,8 @@
variables:
S3_ENDPOINT: "https://s3.embl.de"
S3_BUCKET: "annelids"
JBROWSE_HOSTNAME: "genomes-dev.arendt.embl.de"
RELEASE_LABEL: "dev"
JBROWSE_HOSTNAME: "genomes-testing.arendt.embl.de"
RELEASE_LABEL: "testing"
INGRESS_CLASS: "internal-users"
stages:
......@@ -66,6 +66,11 @@ kustomize_build_apply:
JBROWSE_HOSTNAME: "genomes.arendt.embl.de"
RELEASE_LABEL: "prod"
INGRESS_CLASS: "external-users"
- if: '$CI_COMMIT_REF_NAME == "dev"'
variables:
JBROWSE_HOSTNAME: "genomes-dev.arendt.embl.de"
RELEASE_LABEL: "dev"
INGRESS_CLASS: "internal-users"
- when: always
clean_up_k8s_deployment:
......@@ -87,4 +92,10 @@ clean_up_k8s_deployment:
JBROWSE_HOSTNAME: "genomes.arendt.embl.de"
RELEASE_LABEL: "prod"
INGRESS_CLASS: "external-users"
- when: on_failure
- if: '$CI_COMMIT_REF_NAME == "dev"'
when: on_failure
variables:
JBROWSE_HOSTNAME: "genomes-dev.arendt.embl.de"
RELEASE_LABEL: "dev"
INGRESS_CLASS: "internal-users"
- when: always
name,path
pdumv021,/g/arendt/data/genome_assemblies/pdum-v2.1/genome-assemblies/FINAL_v021_ASM/pdumv021_genome.fa
pmassv1_masked,/g/arendt/data/platynereis_massiliensis/genome/final_assembly/pmassv1.genome.masked.fa
\ No newline at end of file
name,path,display_name
pdumv021,/g/arendt/data/genome_assemblies/pdum-v2.1/genome-assemblies/FINAL_v021_ASM/pdumv021_genome.fa,platychou
pmassv1_masked,/g/arendt/data/platynereis_massiliensis/genome/final_assembly/pmassv1.genome.masked.fa,mid platy
#!/bin/bash
## Gameplan is to parse the genomes and csv files
tail -n +1 tracks.csv |
sort -t , -k 1,2 |
awk -F, '$4=="VCF" { print "jbrowse add-track https://s3.embl.de/annelids/"$1"/variation/"$3".vcf.gz -a \""$1"\" -d \""$6"\" -n \""$3"\" --category \""$5"\""}' >> ../image/jbrowse_script.sh
# Using this to filter above $4=="VCF"
\ No newline at end of file
#
# I am going to assume the CSV files have been patched with the s3 basename path - field 7 for tracks
#
# Genomes
tail -n +1 genomes.csv | # it should not be genomes
sort -t , -k1,1 |
awk -F, '{ print "jbrowse add-assembly https://s3.embl.de/annelids/"$1"/"$2" \
-n \""$1"\" --displayName \""$3"\"" }'
tail -n +1 tracks.csv | # it should not be tracks
sort -t , -k1,1 -k5,5 -k2,2 |
awk -F, '{ print "jbrowse add-track https://s3.embl.de/annelids/"$1"/"$5"/"$3".vcf.gz \
-a \""$1"\" -d \""$6"\" -n \""$3"\" --category \""$5"\""}'
# Text-indices
tail -n +1 tracks.csv |
awk '$1 {print;}'
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