From 543f68f68fd22e1b25d978fe05a07b6d87c75012 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 30 Dec 2020 01:44:13 -0600
Subject: [PATCH] Fix singularity for badges
---
.gitlab-ci.yml | 2 +-
get-updated-badge-info.sh | 14 +++++++-------
2 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f4858d5..bf8e6bc 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -22,7 +22,7 @@ build_badges:
- chmod +x get-updated-badge-info.sh
script:
- echo "Building badges"
- - ./get-updated-badge-info.sh
+ - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' bash get-updated-badge-info.sh
artifacts:
paths:
- badges/
diff --git a/get-updated-badge-info.sh b/get-updated-badge-info.sh
index 32d2def..7309824 100644
--- a/get-updated-badge-info.sh
+++ b/get-updated-badge-info.sh
@@ -1,19 +1,19 @@
#!/bin/bash
echo "collecting stats for badges"
-latest_release_tag=$(singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' git tag --sort=-committerdate -l *.*.* | head -1)
+latest_release_tag=$(git tag --sort=-committerdate -l *.*.* | head -1)
echo "latest_release_tag =" ${latest_release_tag}
-current_pipeline_version=$(singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' git show ${latest_release_tag}:workflow/nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
+current_pipeline_version=$(git show ${latest_release_tag}:workflow/nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
echo "current_pipeline_version =" ${current_pipeline_version}
-current_nextflow_version=$(singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' git show ${latest_release_tag}:workflow/nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')")
+current_nextflow_version=$(git show ${latest_release_tag}:workflow/nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')")
echo "current_nextflow_version =" ${current_nextflow_version}
-master_pipeline_version=$(singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' git show master:workflow/nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
+master_pipeline_version=$(git show master:workflow/nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
echo "master_pipeline_version =" ${master_pipeline_version}
-master_nextflow_version=$(singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' git show master:workflow/nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')")
+master_nextflow_version=$(git show master:workflow/nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')")
echo "master_nextflow_version =" ${master_nextflow_version}
-develop_pipeline_version=$(singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' git show develop:workflow/nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
+develop_pipeline_version=$(git show develop:workflow/nextflow.config | grep -o version.* | grep -oP "(?<=').*(?=')")
echo "develop_pipeline_version =" ${develop_pipeline_version}
-develop_nextflow_version=$(singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' git show develop:workflow/nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')")
+develop_nextflow_version=$(git show develop:workflow/nextflow.config | grep -o nextflowVersion.* | grep -oP "(?<=').*(?=')")
echo "develop_nextflow_version =" ${develop_nextflow_version}
echo "collecting badges"
--
GitLab