Commit 8eba4bb8 authored by David Trudgian's avatar David Trudgian

Basic CI setup

parent 91cd945b
Pipeline #2932 failed with stages
# 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 "$CI_PROJECT_DIR"
# This runs the workflow with test data and does a simple
# check for the expected output files
astrocyte_test:
stage: test
script:
- astrocyte_cli test "$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"
......@@ -57,6 +57,8 @@ workflow_modules:
# file - A single file from user data
# files - One or more files from user data
# select - A selection from a list of values
# multiselect - One or more selections from a list of values
#
# required: true/false, must the parameter be entered/chosen?
# description: A user friendly description of the meaning of the parameter
#
......@@ -107,7 +109,7 @@ workflow_parameters:
# The workflow must publish all final output into $baseDir
# Name of the R module that the vizapp will run against
vizapp_r_module: 'R/3.2.1-intel'
vizapp_r_module: 'R/3.4.1-gccmkl'
# List of any CRAN packages, not provided by the modules, that must be made
# available to the vizapp
......@@ -115,7 +117,13 @@ vizapp_cran_packages:
- shiny
- shinyFiles
# # List of any Bioconductor packages, not provided by the modules, that must be made
# List of any Bioconductor packages, not provided by the modules, that must be made
# available to the vizapp
vizapp_bioc_packages:
- chipseq
-
# List of any packages to install from GitHub using devtools, that must be
# made availavle to the vizapp
vizapp_github_packages:
-
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