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Arendt Group
Jbrowse2 Annelids
Commits
e2a25fb6
Commit
e2a25fb6
authored
10 months ago
by
Cyril Christophe Daniel Robert Cros
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Nextflow work
parent
b3629429
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1 merge request
!6
Nextflow work
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3 changed files
.gitlab-ci.yml
+14
-3
14 additions, 3 deletions
.gitlab-ci.yml
resources_to_s3_NF/genomes.csv
+3
-3
3 additions, 3 deletions
resources_to_s3_NF/genomes.csv
resources_to_s3_NF/jbrowse_script_slug.sh
+18
-5
18 additions, 5 deletions
resources_to_s3_NF/jbrowse_script_slug.sh
with
35 additions
and
11 deletions
.gitlab-ci.yml
+
14
−
3
View file @
e2a25fb6
...
...
@@ -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
This diff is collapsed.
Click to expand it.
resources_to_s3_NF/genomes.csv
+
3
−
3
View file @
e2a25fb6
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
This diff is collapsed.
Click to expand it.
resources_to_s3_NF/jbrowse_script_slug.sh
+
18
−
5
View file @
e2a25fb6
#!/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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