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lskatzlskatz
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restore full test
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‎.github/workflows/unittests.yml

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@@ -69,4 +69,132 @@ jobs:
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spades skesa=2.4 python=3.7 perl-cg-pipeline perl-gd blast prodigal \
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perl-app-cpanminus perl-statistics-descriptive perl-config-simple \
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perl-file-slurp perl-text-levenshtein perl-moo perl-list-moreutils kma=1.4 \
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multiqc fastqc bowtie2 perl-gd perl-gdgraph salmid staramr kalamari taxonkit
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multiqc fastqc bowtie2 perl-gd perl-gdgraph salmid staramr kalamari taxonkit
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- name: check installation
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shell: bash -el {0}
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run: |
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perl -v
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echo
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python -V
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echo
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which perl
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which python
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echo
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which kraken
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kraken --version
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which kraken-build
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echo
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echo conda
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conda info
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echo
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ls -l ~/conda_pkgs_dir /usr/share/miniconda || true
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- name: add some paths to PATH
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run: |
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echo "$GITHUB_WORKSPACE/CG-Pipeline/scripts" >> $GITHUB_PATH
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echo
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cat $GITHUB_PATH
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- name: checkout my repo
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uses: actions/checkout@v4
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with:
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path: SneakerNet
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- name: checkout CG-Pipeline
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uses: actions/checkout@v4
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with:
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repository: lskatz/CG-Pipeline
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path: CG-Pipeline
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ref: v0.5
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- name: apt-get install
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run: |
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sudo apt-get update
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sudo apt-get -y install ca-certificates
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sudo apt-get -y install build-essential sendmail tree
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- name: Cache Kraken DB
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id: cache-kraken
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uses: actions/cache@v4
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with:
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path: |
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/home/runner/conda_pkgs_dir/my-env/share/kalamari-*
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key: kraken-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-perl_v${{ matrix.perl }}--${{env.CACHE_NUMBER}}
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env:
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CACHE_NUMBER: 0
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- name: make very simple kraken database
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if: steps.cache-kraken.outputs.cache-hit != 'true'
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shell: bash -el {0}
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run: |
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which downloadKalamari.sh
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KALAMARI_DEBUG=1 downloadKalamari.sh
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echo "Running buildTaxonomy.sh"
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buildTaxonomy.sh
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echo "Running filterTaxonomy.sh"
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bash -x filterTaxonomy.sh
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echo
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tree $(dirname $(which downloadKalamari.sh))/../share/kalamari-*
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echo
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buildKraken1.sh || echo "ERROR building Kraken1 database with exit code $?"
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- name: Dumper INC
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shell: bash -el {0}
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run: perl -MData::Dumper -e 'print Dumper \@INC'
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- name: tree pwd
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run: tree $(pwd)
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- name: tree home
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run: tree $HOME
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- name: tree GITHUB_WORKSPACE
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run: tree $GITHUB_WORKSPACE
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- name: tree -L 3 -d GITHUB_WORKSPACE
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run: tree -L 3 -d $GITHUB_WORKSPACE
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- name: env
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shell: bash -el {0}
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run: env
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- name: perl-check-dependencies
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shell: bash -el {0}
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run: |
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cd $GITHUB_WORKSPACE/SneakerNet
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perl Makefile.PL
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make
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#cpanm --installdeps . -l $HOME/perl5 --verbose --notest --force
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#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'
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make
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echo "DEBUG: PERL5LIB: $PERL5LIB"
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- name: check-SneakerNet-repo
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shell: bash -el {0}
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run: |
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#eval $(perl -I $HOME/perl5/lib/perl5/ -Mlocal::lib)
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cd $GITHUB_WORKSPACE/SneakerNet
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cat MYMETA.json
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echo;env;echo
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ls -lhS t/M00123-18-001-test/
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md5sum t/M00123-18-001-test/*.fastq.gz
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for i in t/M00123-18-001-test/*.fastq.gz; do echo -ne "$i\t"; zcat $i | tail -n 1; done;
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echo
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echo "PATH broken up:"
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echo "$PATH" | tr ":" "\n"
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echo
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echo "GITHUB_ENV: $GITHUB_ENV"
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cat $GITHUB_ENV
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echo "GITHUB_PATH: $GITHUB_PATH"
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cat $GITHUB_PATH
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echo "Which flash:"
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which flash
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echo
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echo "Running t/00_env.t ..."
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perl t/00_env.t
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for i in t/M00123-18-001-test/*.fastq.gz; do echo -ne "$i\t"; zcat $i | tail -n 1; done;
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- id: prove-lv-t
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name: prove-lv-t
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shell: bash -el {0}
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run: |
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mkdir -v $GITHUB_WORKSPACE/tmp
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export TMPDIR=$GITHUB_WORKSPACE/tmp
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cd $GITHUB_WORKSPACE/SneakerNet
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#sed -i 's+/opt/kraken/full-20140723+/kraken-database+g' config/settings.conf
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sed -i '/KRAKEN_DEFAULT_DB/d' config/settings.conf
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condabin=$(dirname $(which downloadKalamari.sh))
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kalamari_ver=$(downloadKalamari.pl --version)
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kraken_dir="$condabin/../share/kalamari-$kalamari_ver/kalamari-kraken"
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echo $kraken_dir
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ls -lh $kraken_dir
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echo "KRAKEN_DEFAULT_DB $kraken_dir" >> config/settings.conf
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make
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make test
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