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test.yml
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name: Test
on:
push:
branches: [ "master" ]
pull_request:
branches: [ "master" ]
jobs:
build:
strategy:
fail-fast: false
matrix:
os: [ubuntu-20.04, macos-12, macos-11]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v3
- name: Set up Python 3.9.5
uses: actions/setup-python@v4
with:
python-version: 3.9.5
- name: Install dependencies
run: |
python -m pip install --upgrade pip
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
- name: Install coreutils (macOS)
if : ${{ matrix.os == 'macos-12' || matrix.os == 'macos-11' }}
run: |
brew update-reset
brew install coreutils
- name: metafx metafast
run: |
export PATH=bin:$PATH
metafx metafast -t 6 -m 6G -k 31 -i test_data/test/* test_data/3* test_data/4* -b1 200 -b2 5000 -l 50 -w wd_metafast --skip-graph
- name: metafx colored
run: |
export PATH=bin:$PATH
metafx colored -t 6 -m 6G -k 31 -i test_data/sample_list_3.txt --n-comps 100 --perc 0.7 -w wd_colored
- name: metafx chisq (with depth)
run: |
export PATH=bin:$PATH
metafx chisq -t 6 -m 6G -k 31 -i test_data/sample_list.txt -w wd_chisq_4 -n 1000
metafx chisq -t 6 -m 6G -k 31 -i test_data/sample_list_3.txt -w wd_chisq_3 --skip-graph -n 10000 --depth 15
- name: metafx feature_analysis
run: |
export PATH=bin:$PATH
mkdir reads
ln -s `pwd`/test_data/3* reads/
ln -s `pwd`/test_data/4* reads/
ln -s `pwd`/test_data/test/* reads/
metafx feature_analysis -k 31 -t 6 -m 6G -f wd_chisq_4/ -n A_19 -r reads/ --relab 0.5 -w wd_feat_analysis
- name: metafx stats
run: |
export PATH=bin:$PATH
metafx stats -t 6 -m 6G -k 31 -i test_data/sample_list.txt -w wd_stats --skip-graph
- name: metafx metaspades (macOS)
if : ${{ matrix.os == 'macos-12' || matrix.os == 'macos-11' }}
run: |
curl -L https://github.com/ablab/spades/releases/download/v3.15.5/SPAdes-3.15.5-Darwin.tar.gz -o SPAdes-3.15.5-Darwin.tar.gz
tar -zxf SPAdes-3.15.5-Darwin.tar.gz
export PATH=bin:$PATH
export PATH=SPAdes-3.15.5-Darwin/bin/:$PATH
metafx metaspades -t 6 -m 6G -k 31 -i test_data/33* -b1 100 -b2 1000 -l 50 -w wd_metaspades --skip-graph
- name: metafx metaspades (Linux)
if : matrix.os == 'ubuntu-20.04'
run: |
wget https://github.com/ablab/spades/releases/download/v3.15.5/SPAdes-3.15.5-Linux.tar.gz
tar -xzf SPAdes-3.15.5-Linux.tar.gz
export PATH=bin:$PATH
export PATH=SPAdes-3.15.5-Linux/bin/:$PATH
metafx metaspades -t 6 -m 6G -k 31 -i test_data/33* -b1 100 -b2 1000 -l 50 -w wd_metaspades --skip-graph
- name: metafx unique & metafx pca
run: |
export PATH=bin:$PATH
metafx unique -t 6 -m 6G -k 31 -i test_data/sample_list_train.txt -w wd_unique_pca --kmers-dir wd_metafast/kmer-counter-many/kmers
metafx pca -f wd_unique_pca/feature_table.tsv -i wd_unique_pca/samples_categories.tsv --show -w wd_pca
- name: metafx fit (RF & XGB & PyTorch)
run: |
export PATH=bin:$PATH
metafx fit -f wd_unique_pca/feature_table.tsv -i wd_unique_pca/samples_categories.tsv -w wd_fit_rf
metafx fit -f wd_unique_pca/feature_table.tsv -i wd_unique_pca/samples_categories.tsv -w wd_fit_xgb -e XGB
metafx fit -f wd_unique_pca/feature_table.tsv -i wd_unique_pca/samples_categories.tsv -w wd_fit_torch -e Torch
- name: metafx cv
run: |
export PATH=bin:$PATH
metafx cv -f wd_unique_pca/feature_table.tsv -i wd_unique_pca/samples_categories.tsv -w wd_cv -n 2 --grid -t 6
- name: metafx calc_features
run: |
export PATH=bin:$PATH
metafx calc_features -t 6 -m 6G -k 31 -i test_data/test_*.fastq.gz -d wd_unique_pca -w wd_calc_features
- name: metafx predict
run: |
export PATH=bin:$PATH
echo -e "test_A\tA\ntest_B\tB\ntest_C\tC\ntest_D\tD\n" > test_labels.tsv
metafx predict -f wd_calc_features/feature_table.tsv --model wd_cv/rf_model_cv.joblib -w wd_predict -i test_labels.tsv
- name: metafx fit_predict
run: |
export PATH=bin:$PATH
metafx fit_predict -f wd_unique_pca/feature_table.tsv -i wd_unique_pca/samples_categories.tsv -w wd_fit_predict
- name: metafx extract_kmers
run: |
export PATH=bin:$PATH
metafx extract_kmers -t 6 -m 6G -k 31 -i test_data/test/* test_data/3* test_data/4* -w wd_kmers
- name: metafx bandage (macOS)
if : ${{ matrix.os == 'macos-12' || matrix.os == 'macos-11' }}
run: |
mkdir Bandage
cd Bandage
curl -L https://github.com/ctlab/BandageNG/releases/download/continuous/BandageNG-macOS.dmg -o BandageNG
chmod +x BandageNG
cd ..
export PATH=bin:$PATH
export PATH=Bandage/:$PATH
export PATH=SPAdes-3.15.5-Darwin/bin/:$PATH
metafx bandage -w wd_bandage --draw-graph -f wd_unique_pca/ -n 20
- name: metafx bandage (Linux)
if : matrix.os == 'ubuntu-20.04'
run: |
mkdir Bandage
cd Bandage
wget -O BandageNG https://github.com/ctlab/BandageNG/releases/download/continuous/BandageNG-Linux.AppImage
chmod +x BandageNG
cd ..
export PATH=bin:$PATH
export PATH=Bandage/:$PATH
export PATH=SPAdes-3.15.5-Linux/bin/:$PATH
metafx bandage -w wd_bandage --draw-graph -f wd_unique_pca/ -n 20