From 8a1e1a6a5282b28631cf323aa24bf5171d321ab8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 20 Aug 2024 08:53:41 +0200 Subject: [PATCH] fix containers --- .../bd_rhapsody_make_reference/config.vsh.yaml | 12 ++++++------ .../bd_rhapsody_sequence_analysis/config.vsh.yaml | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/src/bd_rhapsody/bd_rhapsody_make_reference/config.vsh.yaml b/src/bd_rhapsody/bd_rhapsody_make_reference/config.vsh.yaml index 82647a1b..b615faa0 100644 --- a/src/bd_rhapsody/bd_rhapsody_make_reference/config.vsh.yaml +++ b/src/bd_rhapsody/bd_rhapsody_make_reference/config.vsh.yaml @@ -135,14 +135,14 @@ engines: packages: [cwlref-runner, cwl-runner] - type: docker run: | - mkdir /var/bd_rhapsody_cwl - cd /var/bd_rhapsody_cwl - git clone https://bitbucket.org/CRSwDev/cwl.git . + mkdir /var/bd_rhapsody_cwl && \ + cd /var/bd_rhapsody_cwl && \ + git clone https://bitbucket.org/CRSwDev/cwl.git . && \ git checkout 8feeace1141b24749ea6003f8e6ad6d3ad5232de - type: docker - run: | - VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1) - echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt + run: + - VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1) + - 'echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt' runners: - type: executable diff --git a/src/bd_rhapsody/bd_rhapsody_sequence_analysis/config.vsh.yaml b/src/bd_rhapsody/bd_rhapsody_sequence_analysis/config.vsh.yaml index c6d1e3a6..6c5b771b 100644 --- a/src/bd_rhapsody/bd_rhapsody_sequence_analysis/config.vsh.yaml +++ b/src/bd_rhapsody/bd_rhapsody_sequence_analysis/config.vsh.yaml @@ -648,14 +648,14 @@ engines: packages: [cwlref-runner, cwl-runner] - type: docker run: | - mkdir /var/bd_rhapsody_cwl - cd /var/bd_rhapsody_cwl - git clone https://bitbucket.org/CRSwDev/cwl.git . + mkdir /var/bd_rhapsody_cwl && \ + cd /var/bd_rhapsody_cwl && \ + git clone https://bitbucket.org/CRSwDev/cwl.git . && \ git checkout 8feeace1141b24749ea6003f8e6ad6d3ad5232de - type: docker - run: | - VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1) - echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt + run: + - VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1) + - 'echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt' test_setup: - type: python packages: [biopython, gffutils]