bump version to 0.27.1 #430
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| name: unit-tests | |
| on: [push] | |
| env: | |
| spadesVer: 3.14.1 | |
| KRAKEN_DEFAULT_DB: /kraken-database | |
| # perl: [ '5.32', '5.30', '5.28' ] | |
| # perl: [ '5.32', '5.30.1', '5.16.3', '5.12.3' ] | |
| # os: ['ubuntu-latest', 'macos-latest', 'windows-latest'] | |
| # https://github.com/marketplace/actions/setup-perl-environment | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ['ubuntu-20.04' ] | |
| perl: [ '5.36.0' ] | |
| python-version: ['3.10'] | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| name: Perl ${{ matrix.perl }} on ${{ matrix.os }} | |
| steps: | |
| - name: Get Date | |
| id: get-date | |
| run: | | |
| today=$(/bin/date -u '+%Y%m%d') | |
| echo $today | |
| echo "today=$today" >> $GITHUB_OUTPUT | |
| - name: set up conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| use-mamba: true | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| channel-priority: strict | |
| channels: conda-forge,bioconda,defaults | |
| mamba-version: "*" | |
| auto-activate-base: true | |
| activate-environment: "~/conda_pkgs_dir/my-env" | |
| use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! | |
| - name: conda info | |
| run: | | |
| conda info | |
| echo | |
| conda list | |
| echo | |
| conda config --show | |
| - name: Cache Conda env | |
| id: cache-conda | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/conda_pkgs_dir | |
| ~/.conda | |
| ~/.condarc | |
| #/usr/share/miniconda | |
| key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-perl_v${{ matrix.perl }}--${{env.CACHE_NUMBER}} | |
| env: | |
| CACHE_NUMBER: 1 | |
| - name: conda installations | |
| shell: bash -el {0} | |
| if: steps.cache-conda.outputs.cache-hit != 'true' | |
| run: | | |
| mamba install -y perl shovill krona samclip flash mash seqtk \ | |
| kmc lighter megahit pilon trimmomatic perl-bioperl kraken=1 \ | |
| spades skesa=2.4 python=3.7 perl-cg-pipeline perl-gd blast prodigal \ | |
| perl-app-cpanminus perl-statistics-descriptive perl-config-simple \ | |
| perl-file-slurp perl-text-levenshtein perl-moo perl-list-moreutils kma=1.4 \ | |
| multiqc fastqc bowtie2 perl-gd perl-gdgraph salmid staramr kalamari taxonkit | |
| - name: check installation | |
| shell: bash -el {0} | |
| run: | | |
| perl -v | |
| echo | |
| python -V | |
| echo | |
| which perl | |
| which python | |
| echo | |
| which kraken | |
| kraken --version | |
| which kraken-build | |
| echo | |
| echo conda | |
| conda info | |
| echo | |
| ls -l ~/conda_pkgs_dir /usr/share/miniconda || true | |
| - name: add some paths to PATH | |
| run: | | |
| echo "$GITHUB_WORKSPACE/CG-Pipeline/scripts" >> $GITHUB_PATH | |
| echo | |
| cat $GITHUB_PATH | |
| - name: checkout my repo | |
| uses: actions/checkout@v4 | |
| with: | |
| path: SneakerNet | |
| - name: checkout CG-Pipeline | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: lskatz/CG-Pipeline | |
| path: CG-Pipeline | |
| ref: v0.5 | |
| - name: apt-get install | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get -y install ca-certificates | |
| sudo apt-get -y install build-essential sendmail tree | |
| - name: Cache Kraken DB | |
| id: cache-kraken | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| /home/runner/conda_pkgs_dir/my-env/share/kalamari-* | |
| key: kraken-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-perl_v${{ matrix.perl }}--${{env.CACHE_NUMBER}} | |
| env: | |
| CACHE_NUMBER: 0 | |
| - name: make very simple kraken database | |
| if: false | |
| #if: steps.cache-kraken.outputs.cache-hit != 'true' | |
| shell: bash -el {0} | |
| run: | | |
| which downloadKalamari.sh | |
| KALAMARI_DEBUG=1 downloadKalamari.sh | |
| echo "Running buildTaxonomy.sh" | |
| buildTaxonomy.sh | |
| echo | |
| tree $(dirname $(which downloadKalamari.sh))/../share/kalamari-* | |
| echo | |
| echo "Running filterTaxonomy.sh" | |
| bash -x filterTaxonomy.sh | |
| echo | |
| tree $(dirname $(which downloadKalamari.sh))/../share/kalamari-* | |
| echo | |
| buildKraken1.sh || echo "ERROR building Kraken1 database with exit code $?" | |
| - name: Dumper INC | |
| shell: bash -el {0} | |
| run: perl -MData::Dumper -e 'print Dumper \@INC' | |
| - name: tree pwd | |
| run: tree $(pwd) | |
| - name: tree home | |
| run: tree $HOME | |
| - name: tree GITHUB_WORKSPACE | |
| run: tree $GITHUB_WORKSPACE | |
| - name: tree -L 3 -d GITHUB_WORKSPACE | |
| run: tree -L 3 -d $GITHUB_WORKSPACE | |
| - name: env | |
| shell: bash -el {0} | |
| run: env | |
| - name: perl-check-dependencies | |
| shell: bash -el {0} | |
| run: | | |
| cd $GITHUB_WORKSPACE/SneakerNet | |
| perl Makefile.PL | |
| make | |
| #cpanm --installdeps . -l $HOME/perl5 --verbose --notest --force | |
| #perl -MData::Dumper -MStatistics::Descriptive -MConfig::Simple -MFile::Slurp -MBio::Kmer -MBio::SeqIO -MText::Fuzzy -MEmail::Stuffer -MBio::FeatureIO -MMoo -MList::MoreUtils -MJSON -e 'print Dumper \%INC' | |
| make | |
| echo "DEBUG: PERL5LIB: $PERL5LIB" | |
| - name: check-SneakerNet-repo | |
| shell: bash -el {0} | |
| run: | | |
| #eval $(perl -I $HOME/perl5/lib/perl5/ -Mlocal::lib) | |
| cd $GITHUB_WORKSPACE/SneakerNet | |
| cat MYMETA.json | |
| echo;env;echo | |
| ls -lhS t/M00123-18-001-test/ | |
| md5sum t/M00123-18-001-test/*.fastq.gz | |
| for i in t/M00123-18-001-test/*.fastq.gz; do echo -ne "$i\t"; zcat $i | tail -n 1; done; | |
| echo | |
| echo "PATH broken up:" | |
| echo "$PATH" | tr ":" "\n" | |
| echo | |
| echo "GITHUB_ENV: $GITHUB_ENV" | |
| cat $GITHUB_ENV | |
| echo "GITHUB_PATH: $GITHUB_PATH" | |
| cat $GITHUB_PATH | |
| echo "Which flash:" | |
| which flash | |
| echo | |
| echo "Running t/00_env.t ..." | |
| perl t/00_env.t | |
| for i in t/M00123-18-001-test/*.fastq.gz; do echo -ne "$i\t"; zcat $i | tail -n 1; done; | |
| - id: prove-lv-t | |
| name: prove-lv-t | |
| shell: bash -el {0} | |
| run: | | |
| mkdir -v $GITHUB_WORKSPACE/tmp | |
| export TMPDIR=$GITHUB_WORKSPACE/tmp | |
| cd $GITHUB_WORKSPACE/SneakerNet | |
| #sed -i 's+/opt/kraken/full-20140723+/kraken-database+g' config/settings.conf | |
| sed -i '/KRAKEN_DEFAULT_DB/d' config/settings.conf | |
| condabin=$(dirname $(which downloadKalamari.sh)) | |
| kalamari_ver=$(downloadKalamari.pl --version) | |
| kraken_dir="$condabin/../share/kalamari-$kalamari_ver/kalamari-kraken" | |
| echo $kraken_dir | |
| ls -lh $kraken_dir || echo "ERROR: could not ls $kraken_dir" | |
| echo "KRAKEN_DEFAULT_DB $kraken_dir" >> config/settings.conf | |
| make | |
| make test | |