.gitlab-ci.yml 1.24 KB
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# Run our tests against a specific version of astrocyte
before_script:
  - module load astrocyte/0.1.0

stages:
    - check
    - test

# This performs validation of the astrocyte_pkg.yml file
astrocyte_check:
  stage: check
  script:
  - astrocyte_cli check "$CI_PROJECT_DIR"

# This runs the workflow with test data and does a simple
# check for the expected output files
astrocyte_test:
  stage: test
  script:
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  - cd "$CI_PROJECT_DIR/test_data"
  - sh fetch_test_data.sh
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  - astrocyte_cli test "$CI_PROJECT_DIR"
  - test -s "$CI_PROJECT_DIR/workflow/output/G1E_ER4_CTCT_chr9.fastq.sam.gz.bam"
  - test -s "$CI_PROJECT_DIR/workflow/output/G1E_ER4_CTCT_chr9.fastq.sam.gz.bam_bwa_nomodel_peaks.bed"
  - test -s "$CI_PROJECT_DIR/workflow/output/G1E_ER4_CTCT_chr9.fastq.sam.gz.bam_bwa_nomodel_peaks.xls"
  - test -s "$CI_PROJECT_DIR/workflow/output/G1E_ER4_CTCT_chr9.fastq.sam.gz.bam_bwa_nomodel_summits.bed"

# This verifies we can install the shiny vizapp dependencies, set the vizapp
# running and make at least a connection to it.
astrocyte_shiny:
  stage: test
  script:
  - astrocyte_cli shiny-prepare "$CI_PROJECT_DIR"
  - 'timeout 10 astrocyte_cli shiny "$CI_PROJECT_DIR" &'
  - sleep 5
  - unset http_proxy
  - unset all_proxy
  - wget "http://127.0.0.1:8123"