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main.yml
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name: GitHub Actions CI
on:
push:
branches: [ master, experimental, develop ]
paths-ignore:
- '**.md'
workflow_dispatch:
jobs:
make-tests:
name: Make
strategy:
matrix:
machine: [ubuntu-latest, macOS-12]
runs-on: ['${{ matrix.machine }}']
env:
REF_DIR: ./test/adeno_fiber
INPUT: ./test/adeno_fiber/adeno_fiber
steps:
- uses: actions/checkout@v4
with:
submodules: recursive
- name: make
run: |
g++ --version
make -j
- name: copy sl->slink references
run: |
cp ./test/adeno_fiber/sl.fasta ./test/adeno_fiber/slink.fasta
cp ./test/hemopexin/medoid-sl.fasta ./test/hemopexin/medoid-slink.fasta
- name: tar artifacts
run: tar -cvf famsa.tar ./famsa ./test
- uses: actions/upload-artifact@v4
with:
name: executable-artifact-${{ matrix.machine }}
path: ./famsa.tar
########################################################################################
full-tree:
name: Full tree (adeno-fiber)
needs: make-tests
strategy:
fail-fast: false
matrix:
tree: [sl, upgma]
machine: [ubuntu-latest, macOS-12]
runs-on: ['${{ matrix.machine }}']
env:
REF_DIR: ./test/adeno_fiber
INPUT: ./test/adeno_fiber/adeno_fiber
steps:
- uses: actions/download-artifact@v4
with:
name: executable-artifact-${{ matrix.machine }}
path: ./
- name: untar artifacts
run: tar -xf famsa.tar
- name: ${{matrix.tree}} (tree only)
run: |
./famsa -v -gt ${{matrix.tree}} -gt_export ${INPUT} ${{matrix.tree}}.dnd
cmp ${{matrix.tree}}.dnd ${REF_DIR}/${{matrix.tree}}.dnd
- name: ${{matrix.tree}} (from tree)
run: |
./famsa -v -gt import ${{matrix.tree}}.dnd ${INPUT} ${{matrix.tree}}.dnd.fasta
cmp ${{matrix.tree}}.dnd.fasta ${REF_DIR}/${{matrix.tree}}.fasta
- name: ${{matrix.tree}} (complete alignment)
run: |
./famsa -v -gt ${{matrix.tree}} ${INPUT} ${{matrix.tree}}.fasta
cmp ${{matrix.tree}}.fasta ${REF_DIR}/${{matrix.tree}}.fasta
########################################################################################
medoid-tree:
name: Medoid tree (hemopexin)
needs: full-tree
strategy:
fail-fast: false
matrix:
tree: [sl, upgma, nj]
machine: [ubuntu-latest, macOS-12]
runs-on: ['${{ matrix.machine }}']
env:
REF_DIR: ./test/hemopexin
INPUT: ./test/hemopexin/hemopexin
steps:
- uses: actions/download-artifact@v4
with:
name: executable-artifact-${{ matrix.machine }}
path: ./
- name: untar artifacts
run: tar -xf famsa.tar
- name: medoid + ${{matrix.tree}} (tree only)
run: |
./famsa -medoidtree -gt ${{matrix.tree}} -gt_export ${INPUT} medoid-${{matrix.tree}}.dnd
cmp medoid-${{matrix.tree}}.dnd ${REF_DIR}/medoid-${{matrix.tree}}.dnd
- name: medoid + ${{matrix.tree}} (complete alignment)
run: |
./famsa -medoidtree -gt ${{matrix.tree}} ${INPUT} medoid-${{matrix.tree}}.fasta
cmp medoid-${{matrix.tree}}.fasta ${REF_DIR}/medoid-${{matrix.tree}}.fasta
- name: medoid + ${{matrix.tree}} (from tree)
run: |
./famsa -gt import medoid-${{matrix.tree}}.dnd ${INPUT} medoid-${{matrix.tree}}.dnd.fasta
cmp medoid-${{matrix.tree}}.dnd.fasta ${REF_DIR}/medoid-${{matrix.tree}}.fasta
- name: medoid + ${{matrix.tree}} (non-default params)
run: |
./famsa -medoidtree -gt ${{matrix.tree}} -gt_export -subtree_size 10 -sample_size 100 -cluster_fraction 0.2 -cluster_iters 1 ${INPUT} medoid-${{matrix.tree}}-params.dnd
cmp medoid-${{matrix.tree}}-params.dnd ${REF_DIR}/medoid-${{matrix.tree}}-params.dnd
########################################################################################
other-tests:
name: Other tests (adeno-fiber)
needs: medoid-tree
strategy:
fail-fast: false
matrix:
machine: [ubuntu-latest, macOS-12]
runs-on: ['${{ matrix.machine }}']
env:
REF_DIR: ./test/adeno_fiber
INPUT: ./test/adeno_fiber/adeno_fiber
steps:
- uses: actions/download-artifact@v4
with:
name: executable-artifact-${{ matrix.machine }}
path: ./
- name: untar artifacts
run: tar -xf famsa.tar
- name: non-default gaps
run: |
./famsa -go 10 -ge 2 -tgo 0.5 -tge 1.0 -gsd 3 -gsl 30 ${INPUT} gaps.fasta
cmp gaps.fasta ${REF_DIR}/gaps.fasta
- name: export distance
run: |
./famsa -dist_export ${INPUT} dist.csv
cmp dist.csv ${REF_DIR}/dist.csv
- name: export distance (square)
run: |
./famsa -dist_export -square_matrix ${INPUT} dist_sq.csv
cmp dist_sq.csv ${REF_DIR}/dist_sq.csv
- name: export pid
run: |
./famsa -dist_export -pid ${INPUT} pid.csv
cmp pid.csv ${REF_DIR}/pid.csv
- name: export pid (square)
run: |
./famsa -dist_export -square_matrix -pid ${INPUT} pid_sq.csv
cmp pid_sq.csv ${REF_DIR}/pid_sq.csv
########################################################################################