salmon/.github/workflows/ci.yml at 5f366124fc619e5962825c79f4a2d7ac6ad091f1 · COMBINE-lab/salmon · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
name: CI

on:
  push:
    branches:
      - "**"
  workflow_dispatch:

permissions:
  contents: read

jobs:
  precheck:
    runs-on: ubuntu-latest
    outputs:
      run_ci: ${{ steps.decide.outputs.run_ci }}
    steps:
      - id: decide
        shell: bash
        run: |
          set -euo pipefail
          msg="$(jq -r '.head_commit.message // ""' "$GITHUB_EVENT_PATH")"
          ref="${GITHUB_REF#refs/heads/}"
          run_ci=false

          if [[ "${GITHUB_EVENT_NAME}" == "workflow_dispatch" ]]; then
            run_ci=true
          fi
          if [[ "$ref" == "main" ]]; then
            run_ci=true
          fi
          if [[ "$msg" == *"[run-ci]"* ]]; then
            run_ci=true
          fi

          {
            echo "run_ci=$run_ci"
          } >> "$GITHUB_OUTPUT"

  build-test:
    needs: precheck
    if: ${{ needs.precheck.outputs.run_ci == 'true' }}
    runs-on: ${{ matrix.os }}
    timeout-minutes: 120
    strategy:
      fail-fast: false
      matrix:
        include:
          - os: ubuntu-22.04
            target_id: linux-x86_64
            build_parallel: 2
          - os: ubuntu-24.04-arm
            target_id: linux-aarch64
            build_parallel: 2
          - os: macos-15-intel
            target_id: macos-x86_64
            build_parallel: 3
          - os: macos-14
            target_id: macos-arm64
            build_parallel: 3
    steps:
      - uses: actions/checkout@v4

      - name: Install Linux Build Dependencies
        if: runner.os == 'Linux'
        run: |
          sudo apt-get update
          sudo apt-get install -y \
            build-essential \
            cmake \
            git \
            curl \
            libcurl4-openssl-dev \
            libbz2-dev \
            liblzma-dev

      - name: Configure
        run: |
          cmake -S . -B build-ci \
            -DCMAKE_BUILD_TYPE=Release \
            -DSALMON_ENABLE_TESTS=ON \
            -DSALMON_USE_SYSTEM_DEPS=OFF \
            -DSALMON_FETCH_MISSING_DEPS=ON \
            -DSALMON_BOOST_USE_STATIC_LIBS=ON

      - name: Build
        run: cmake --build build-ci --target salmon unitTests --parallel ${{ matrix.build_parallel }}

      - name: Run Unit Tests
        run: ./build-ci/src/unitTests

      - name: CLI Smoke
        run: ./build-ci/src/salmon -h

      - name: Prepare Sample Data
        shell: bash
        run: |
          set -euo pipefail
          if [[ ! -d sample_data ]]; then
            tar -xzf sample_data.tgz
          fi

      - name: Sample Data Smoke (Mapping)
        run: |
          ./build-ci/src/salmon index \
            -t sample_data/transcripts.fasta \
            -i build-ci/sample_index
          ./build-ci/src/salmon quant \
            -l A \
            -i build-ci/sample_index \
            -1 sample_data/reads_1.fastq \
            -2 sample_data/reads_2.fastq \
            -o build-ci/sample_quant_mapping

      - name: Sample Data Smoke (Alignment)
        run: |
          ./build-ci/src/salmon quant \
            -l A \
            -t sample_data/transcripts.fasta \
            -a sample_data/sample_alignments.bam \
            -o build-ci/sample_quant_alignment

      - name: Package Binary Artifact
        shell: bash
        run: |
          set -euo pipefail
          pkg_dir="release/salmon-${{ matrix.target_id }}"
          mkdir -p "$pkg_dir/bin"
          cp build-ci/src/salmon "$pkg_dir/bin/"
          cp LICENSE "$pkg_dir/"
          cp README.md "$pkg_dir/"
          tar -C release -czf "salmon-${{ matrix.target_id }}.tar.gz" "salmon-${{ matrix.target_id }}"

      - name: Upload Binary Artifact
        uses: actions/upload-artifact@v4
        with:
          name: salmon-${{ matrix.target_id }}
          path: salmon-${{ matrix.target_id }}.tar.gz
          if-no-files-found: error