Github workflows added

refresh-bio · Sep 5, 2024 · f9725b7 · f9725b7
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diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -0,0 +1,77 @@
+name: Deploy
+
+on:
+ release:
+    types:
+      - created
+
+jobs:
+
+
+ ########################################################################################
+  checkout:
+    name: Checkout
+    strategy:
+      matrix:
+        machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
+    runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+
+########################################################################################
+  make:
+    name: Make
+    needs: checkout
+    strategy:
+      fail-fast: false
+      matrix:
+        machine: [x64_linux, arm64_linux, x64_mac, arm64_mac]
+
+    runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']  
+
+    steps:
+    - name: make 
+      run: |
+        make clean
+        make -j32 CXX=g++-12
+    - name: tar artifacts
+      run: tar -cvzf lz-ani.tar.gz lz-ani LICENSE
+
+
+########################################################################################
+  help:
+    name: Print usage
+    needs: make
+    strategy:
+      fail-fast: false
+      matrix:
+        machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
+    runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
+
+    steps:
+    - name: help
+      run: ./lz-ani
+
+########################################################################################
+  upload:
+    name: Upload
+    needs: help
+    strategy:
+      fail-fast: false
+      matrix:
+        machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
+    runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
+
+    steps:
+    - name: deploy
+      uses: actions/upload-release-asset@v1.0.1
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        upload_url: ${{ github.event.release.upload_url }}
+        asset_path: ./lz-ani.tar.gz
+        asset_name: lz-ani-${{ github.event.release.tag_name }}-${{matrix.machine}}.tar.gz
+        asset_content_type: application/gzip
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -0,0 +1,62 @@
+name: GitHub Actions CI
+
+on:
+  push:
+    branches: [ master, develop, main]
+    paths-ignore:
+      - '**.md'
+  workflow_dispatch:
+
+jobs:
+
+########################################################################################
+  make:
+    name: Make
+    strategy:
+      fail-fast: false
+      matrix:
+        machine: [ubuntu-latest, macOS-12]
+    runs-on: ['${{ matrix.machine }}']   
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: make
+      run: | 
+        g++ --version
+        make -j CXX=g++-12
+
+    - name: tar artifacts
+      run: tar -cvf lz-ani.tar ./lz-ani ./test
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: executable-artifact-${{ matrix.machine }}
+        path: ./lz-ani.tar    
+
+########################################################################################
+  vir61:
+    needs: make
+    name: Virus data
+    strategy:
+      fail-fast: false
+      matrix:
+        machine: [ubuntu-latest, macOS-12]
+    runs-on: ['${{ matrix.machine }}']
+
+    steps:
+    - uses: actions/download-artifact@v4
+      with:
+        name: executable-artifact-${{ matrix.machine }}
+        path: ./
+
+    - name: untar artifacts
+      run: |
+        tar -xf lz-ani.tar
+    
+    - name: build 
+      run: |
+        ./lz-ani all2all --in-dir ./test/vir61 --out ani.tsv
+        cmp ani.tsv ./test/vir61.ani.tsv
+
diff --git a/.github/workflows/self-hosted.yml b/.github/workflows/self-hosted.yml
@@ -0,0 +1,83 @@
+name: Self-hosted CI
+
+on:
+  pull_request:
+    branches: [ master, develop, main ]
+    paths-ignore:
+      - '**.md'
+  workflow_dispatch:
+
+jobs:
+
+ ########################################################################################
+  checkout:
+    name: Checkout
+    strategy:
+      matrix:
+        machine: [tripper, arm64_linux, mac-i7, mac-m1]
+    runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+
+
+########################################################################################
+  make:
+    name: Make
+    needs: checkout
+    strategy:
+      fail-fast: false
+      matrix:
+        machine: [tripper, arm64_linux, mac-i7, mac-m1]
+        compiler: [12]
+    runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']  
+
+    steps:
+    - name: make (g++-${{matrix.compiler}})
+      run: | 
+        make -j32 CXX=g++-${{matrix.compiler}} 
+        cp ./lz-ani ./lz-ani-${{matrix.compiler}}
+        make clean
+        
+########################################################################################
+  help:
+    name: Print usage
+    needs: make
+    strategy:
+      fail-fast: false
+      matrix:
+        machine: [tripper, arm64_linux, mac-i7, mac-m1]
+        compiler: [12]
+    runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
+
+    env: 
+      EXEC: ./lz-ani-${{matrix.compiler}}
+
+    steps:
+    - name: help (g++-${{matrix.compiler}})
+      run: | 
+       ${EXEC} 
+
+
+ ########################################################################################
+  vir61:
+    name: Vir61
+    needs: help
+    strategy:
+      fail-fast: false
+      matrix:
+        machine: [tripper, arm64_linux, mac-i7, mac-m1]
+        compiler: [12]
+    runs-on: [self-hosted, lz-ani, '${{ matrix.machine }}']
+
+    env: 
+      EXEC: ./lz-ani-${{matrix.compiler}}
+
+    steps:
+
+    - name: all2all 
+      run: |
+        ${EXEC} all2all --in-dir ./test/vir61 --out ani.tsv
+        cmp ani.tsv ./test/vir61.ani.tsv
diff --git a/README.md b/README.md
@@ -1,4 +1,9 @@
 # LZ-ANI
+
+![version](https://img.shields.io/badge/version-1.1.0-blue.svg)
+[![GitHub Actions CI](../../workflows/GitHub%20Actions%20CI/badge.svg)](../../actions/workflows/main.yml)
+[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
+
 LZ-ANI is a fast and memory-efficient tool for determining average nucleotide identity (ANI) in large sets of genomic sequences. The tool uses Lempel-Ziv parsing, achieving high sensitivity in discerning matched and mismatched nucleotides, thereby enabling accurate determination of ANI. Its efficiency stems from a simplified indel handling model, making LZ-ANI magnitudes faster than alignment-based tools (e.g., BLASTn, MegaBLAST) while maintaining accuracy comparable to the most sensitive BLASTn searches. 
 
 LZ-ANI is a key component of [Vclust](https://github.com/refresh-bio/vclust), a tool for comparing and clustering virus genomes. Although optimized for virus genomes, LZ-ANI's parameters can be customized for longer genomes, such as those of bacteria and archaea.

diff --git a/test/vir61.ani.ids.tsv b/test/vir61.ani.ids.tsv
@@ -0,0 +1,62 @@
+id	seq_len	no_parts
+NC_020483.1	42084	1
+NC_028800.1	41698	1
+NC_023005.1	41386	1
+NC_011043.1	41181	1
+NC_028661.1	41149	1
+NC_013647.1	41119	1
+NC_028977.1	41054	1
+NC_015264.1	40973	1
+NC_015719.1	40940	1
+NC_028822.1	40829	1
+NC_028863.1	40477	1
+NC_024362.1	40472	1
+NC_031943.1	40470	1
+NC_023736.1	40411	1
+NC_021062.1	40192	1
+NC_028688.1	40114	1
+NC_001604.1	39937	1
+NC_022744.1	39860	1
+NC_011040.1	39816	1
+NC_007456.1	39704	1
+NC_031258.1	39696	1
+NC_023548.1	39651	1
+NC_031115.1	39616	1
+NC_001271.1	39600	1
+NC_015208.1	39562	1
+NC_007149.1	39503	1
+NC_011534.1	39472	1
+NC_031123.1	39444	1
+NC_031066.1	39434	1
+NC_019510.1	39282	1
+NC_031018.1	39274	1
+NC_015249.1	39270	1
+NC_011042.1	39252	1
+NC_028655.1	39235	1
+NC_031114.1	39235	1
+NC_023576.1	39207	1
+NC_027292.1	39167	1
+NC_015159.1	39162	1
+NC_031092.1	39158	1
+NC_028772.1	39133	1
+NC_024379.1	39093	1
+NC_031937.1	38979	1
+NC_023558.1	38966	1
+NC_011045.1	38841	1
+NC_010807.1	38815	1
+NC_027387.1	38810	1
+NC_011038.1	38677	1
+NC_025451.1	38646	1
+NC_028880.1	38625	1
+NC_023715.1	38616	1
+NC_008694.1	38564	1
+NC_019416.1	38513	1
+NC_013651.1	38497	1
+NC_011085.3	38457	1
+NC_015271.1	38368	1
+NC_003298.1	38208	1
+NC_028702.1	38084	1
+NC_004777.1	37555	1
+NC_004665.1	37359	1
+NC_029102.1	36051	1
+NC_028795.1	31522	1