LINKS/azure-pipelines.yml at master · BirolLab/LINKS · GitHub

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# Starter pipeline
# Start with a minimal pipeline that you can customize to build and deploy your code.
# Add steps that build, run tests, deploy, and more:
# https://aka.ms/yaml

pool:
  vmImage: ubuntu-latest

jobs:
- job: Test
  steps:
  - script: |
      mkdir -p ~/miniforge3
      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh  -o ~/miniforge3/miniforge.sh
      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
      rm -rf  ~/miniforge3/miniforge.sh
      ~/miniforge3/bin/conda init bash
      ~/miniforge3/bin/conda init zsh
      export CONDA=$(realpath ~/miniforge3/bin)
      echo "##vso[task.prependpath]$CONDA"
    displayName: Install conda

  - script: conda create --yes --quiet --name links_ci
    displayName: Create Anaconda environment

  - script: |
      mamba install -c bioconda --yes --quiet --name links_ci compilers make autoconf automake libtool pkg-config perl wget
    displayName: Install dependencies
  - script: |
      conda activate links_ci
      git submodule init
      git submodule update
      ./autogen.sh
      ./configure
      make
    displayName: Compile LINKS
  - script: |
      conda activate links_ci
      mkdir CI_TEST && cd CI_TEST
      wget http://www.bcgsc.ca/downloads/supplementary/LINKS/K12_full2dONT_longread.fa
      wget http://www.bcgsc.ca/downloads/supplementary/LINKS/ecoliK12_abyss_illumina_contig_baseline.fa
      echo K12_full2dONT_longread.fa >> K12_F2D.fof
    displayName: Download test files
  - script: |
      conda activate links_ci
      export PATH=$(pwd)/src:$(pwd)/bin:$PATH
      cd CI_TEST
      LINKS_CPP -f ecoliK12_abyss_illumina_contig_baseline.fa -s K12_F2D.fof -d 4000 -k 15 -t 2 -o 0 -e 0.1 -z 500 -p 0.001 -b CI_TEST_1 -v 1 -x 0
    displayName: Run test on C++ binary
  - script: |
      conda activate links_ci
      export PATH=$(pwd)/src:$(pwd)/bin:$PATH
      cd CI_TEST
      LINKS -f ecoliK12_abyss_illumina_contig_baseline.fa -s K12_F2D.fof -d 4000 -k 15 -t 2 -o 0 -e 0.1 -z 500 -p 0.001 -b CI_TEST_2 -v 1 -x 0
    displayName: Run test on Makefile wrapper shell script
  - script: |
      conda activate links_ci
      export PATH=$(pwd)/src:$(pwd)/bin:$PATH
      cd tests
      ./run_me.sh
      diff <(sort -k1,1 -k2,2n -k3,3n -k4,4n -k5,5n installation_test.tigpair_checkpoint.tsv) <(sort -k1,1 -k2,2n -k3,3n -k4,4n -k5,5n ./expected_outputs/installation_test.tigpair_checkpoint.tsv)
      diff <(sort -k1,1 -k2,2n -k3,3n -k4,4n -k5,5n installation_test.scaffolds.fa) <(sort -k1,1 -k2,2n -k3,3n -k4,4n -k5,5n ./expected_outputs/installation_test.scaffolds.fa)
    displayName: Run installation test and compare