From 00eb7f471baa98f1e6b17fe6aa0dc77b8d4297da Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 21 Mar 2021 12:34:04 -0500
Subject: [PATCH] Use base singularity for env latest get
---
.gitlab-ci.yml | 10 ++++++++--
1 file changed, 8 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index da81bec..c35c463 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1041,13 +1041,16 @@ dnanexus:
script:
- hostname
- ulimit -a
+ - baseImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep gudmap-rbk_base | cut -d"/" -f2 | cut -d":" -f1)
+ - baseVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep gudmap-rbk_base | cut -d"/" -f2 | cut -d":" -f2)
+ - echo ${dir}${baseImg}_${baseVar}.sif
+ - latest_release_tag=$(singularity run ${dir}${baseImg}_${baseVar}.sif git tag --sort=-committerdate -l *.*.* | head -1)
- mkdir -p ./badges/env
- curl --request GET https://img.shields.io/badge/Envronment%3A%20DNAnexus-inactive-critical?style=flat > ./badges/env/dnanexus.svg
- module load dxtoolkit/python27/0.294.0
- export NXF_XPACK_LICENSE=${nxf_license}
- dx upload ./test_data/auth/c* --path /ci-env/auth/ --parents --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace}
- dx upload ./test_data/fastq/xsmall/Q-Y5F6_10K.R{1,2}.fastq.gz --path /ci-env/input/ --parents --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace}
- - latest_release_tag=$(git tag --sort=-committerdate -l *.*.* | head -1)
- >
dx run nf-dxapp-bicf --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace} \
--delay-workspace-destruction \
@@ -1086,6 +1089,10 @@ aws:
script:
- hostname
- ulimit -a
+ - baseImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep gudmap-rbk_base | cut -d"/" -f2 | cut -d":" -f1)
+ - baseVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep gudmap-rbk_base | cut -d"/" -f2 | cut -d":" -f2)
+ - echo ${dir}${baseImg}_${baseVar}.sif
+ - latest_release_tag=$(singularity run ${dir}${baseImg}_${baseVar}.sif git tag --sort=-committerdate -l *.*.* | head -1)
- mkdir -p ./badges/env
- curl --request GET https://img.shields.io/badge/Envronment%3A%20AWS-inactive-critical?style=flat > ./badges/env/aws.svg
- module load awscli/1.11.139
@@ -1094,7 +1101,6 @@ aws:
- aws configure set region ${aws_region}
- aws s3 cp ./test_data/auth/ s3://bicf-output/ci-env/auth/ --exclude "*" --include "c*" --recursive
- aws s3 cp ./test_data/fastq/xsmall/ s3://bicf-output/ci-env/input/ --exclude "*" --include "Q-Y5F6_10K.R*.fastq.gz" --recursive
- - latest_release_tag=$(git tag --sort=-committerdate -l *.*.* | head -1)
- >
id=$(aws batch submit-job\
--job-name nf-GUDMAP_RBK_ci-env\
--
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