From 0147ece8593ee5edd1badec79287207ace643106 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 9 Dec 2019 16:33:28 -0600
Subject: [PATCH] Upgrade docker images (gudmaprbkfilexfer and trimgalore) to
1.1
---
.gitlab-ci.yml | 4 ++--
workflow/conf/biohpc.config | 6 +++---
workflow/conf/conda.env.bdbag.yml | 5 -----
3 files changed, 5 insertions(+), 10 deletions(-)
delete mode 100644 workflow/conf/conda.env.bdbag.yml
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b69d702..1181343 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -11,6 +11,6 @@ stages:
unit:
stage: unit
script:
- - singularity run 'docker://bicf/bdbag:1.0' bdbag --materialize ./test_data/File_Q-Y53P.zip
- - singularity run 'docker://bicf/bdbag:1.0' bdbag --validate full ./test_data/File_Q-Y53P/
+ - singularity run 'docker://bicf/gudmaprbkfilexfer:1.1' bdbag --materialize ./test_data/File_Q-Y53P.zip
+ - singularity run 'docker://bicf/gudmaprbkfilexfer:1.1' bdbag --validate full ./test_data/File_Q-Y53P/
- if [[ $(md5sum test_data/File_Q-Y53P/data/assets/Study/Q-Y4H0/Experiment/Q-Y4BY/Replicate/Q-Y5F8/hMARIS_SIX2+_RiboDep#1.gene.rpkm.txt | awk '{ print $1 }') != $(cat test_data/File_Q-Y53P/data/File.csv | cut -d ',' -f10 | tail -1) ]]; then exit 21; fi;
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 2e90c4f..13368ad 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -5,13 +5,13 @@ process {
// Process specific configuration
withName:splitData {
- container = 'docker://bicf/gudmaprbkfilexfer:1.0'
+ container = 'docker://bicf/gudmaprbkfilexfer:1.1'
}
withName:getData {
- container = 'docker://bicf/gudmaprbkfilexfer:1.0'
+ container = 'docker://bicf/gudmaprbkfilexfer:1.1'
}
withName:trimData {
- container = 'docker://bicf/trimgalore:1.0'
+ container = 'docker://bicf/trimgalore:1.1'
queue = '256GB,256GBv1,384GB'
}
}
diff --git a/workflow/conf/conda.env.bdbag.yml b/workflow/conf/conda.env.bdbag.yml
deleted file mode 100644
index 33361d3..0000000
--- a/workflow/conf/conda.env.bdbag.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-name: bdbag
-dependencies:
- - pandas=0.23.3=py36_0
- - pip:
- - bdbag==1.5.5
--
GitLab