From 57b8970e88523c5d6815d4a5fb63a61ad2582839 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 28 Dec 2020 18:47:27 -0600
Subject: [PATCH] Fix wrong container for deriva in ci
---
.gitlab-ci.yml | 28 ++++++++++++++--------------
1 file changed, 14 insertions(+), 14 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 20a3e7a..ac26333 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -29,8 +29,8 @@ getBag:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
- - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' deriva-download-cli --version > version_deriva.txt
- - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6
+ - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-download-cli --version > version_deriva.txt
+ - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6
- pytest -m getBag
artifacts:
name: "$CI_JOB_NAME"
@@ -47,10 +47,10 @@ getData:
except:
- merge_requests
script:
- - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' bdbag --version > version_bdbag.txt
+ - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag --version > version_bdbag.txt
- ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- unzip ./test_data/bag/staging/Q-Y5F6_inputBag.zip
- - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6 Q-Y5F6 TEST
+ - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6 Q-Y5F6 TEST
- pytest -m getData
artifacts:
name: "$CI_JOB_NAME"
@@ -205,12 +205,12 @@ countData:
script:
- ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/geneID.tsv
- ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/Entrez.tsv
- - singularity run 'docker://bicf/subread2:2.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o Q-Y5F6_1M.se.countData -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam
- - singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se.countData
- - singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID Q-Y5F6_1M.se
+ - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o Q-Y5F6_1M.se.countData -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam
+ - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se.countData
+ - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID Q-Y5F6_1M.se
- assignedReads=$(grep -m 1 'Assigned' *.summary | grep -oe '\([0-9.]*\)')
- - singularity run 'docker://bicf/subread2:2.0.0' featureCounts -v &> version_featurecounts.txt
- - singularity run 'docker://bicf/subread2:2.0.0' R --version > version_r.txt
+ - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' featureCounts -v &> version_featurecounts.txt
+ - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' R --version > version_r.txt
- pytest -m makeFeatureCounts
artifacts:
name: "$CI_JOB_NAME"
@@ -228,8 +228,8 @@ makeBigWig:
except:
- merge_requests
script:
- - singularity run 'docker://bicf/deeptools3.3:2.0.1_indev' deeptools --version > version_deeptools.txt
- - singularity run 'docker://bicf/deeptools3.3:2.0.1_indev' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam -o Q-Y5F6_1M.se.bw
+ - singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' deeptools --version > version_deeptools.txt
+ - singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam -o Q-Y5F6_1M.se.bw
- pytest -m makeBigWig
artifacts:
name: "$CI_JOB_NAME"
@@ -246,8 +246,8 @@ fastqc:
except:
- merge_requests
script:
- - singularity run 'docker://bicf/fastqc:2.0.1_indev' fastqc --version > version_fastqc.txt
- - singularity run 'docker://bicf/fastqc:2.0.1_indev' fastqc ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -o .
+ - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc --version > version_fastqc.txt
+ - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -o .
- pytest -m fastqc
artifacts:
name: "$CI_JOB_NAME"
@@ -409,7 +409,7 @@ generateVersions:
except:
- merge_requests
script:
- - singularity run 'docker://bicf/multiqc1.8:2.0.1_indev' multiqc --version > version_multiqc.txt
+ - singularity run 'docker://gudmaprbk/multiqc1.9:1.0.0' multiqc --version > version_multiqc.txt
- python ./workflow/scripts/generate_versions.py -o software_versions
- python ./workflow/scripts/generate_references.py -r ./docs/references.md -o software_references
artifacts:
--
GitLab