force cache with taxonkit

.github/workflows/unittests.yml

@@ -59,7 +59,7 @@ jobs:
             #/usr/share/miniconda
           key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-perl_v${{ matrix.perl }}--${{env.CACHE_NUMBER}}
         env:
-          CACHE_NUMBER: 7
+          CACHE_NUMBER: 1
       - name: conda installations
         shell: bash -el {0}
         if: steps.cache-conda.outputs.cache-hit != 'true'
@@ -69,132 +69,4 @@ jobs:
             spades skesa=2.4 python=3.7 perl-cg-pipeline perl-gd blast prodigal \
             perl-app-cpanminus perl-statistics-descriptive perl-config-simple \
             perl-file-slurp perl-text-levenshtein perl-moo perl-list-moreutils kma=1.4 \
-            multiqc fastqc bowtie2 perl-gd perl-gdgraph salmid staramr kalamari
-      - name: check installation
-        shell: bash -el {0}
-        run: | 
-          perl -v
-          echo 
-          python -V
-          echo 
-          which perl
-          which python
-          echo
-          which kraken
-          kraken --version
-          which kraken-build
-          echo
-          echo conda
-          conda info
-          echo
-          ls -l ~/conda_pkgs_dir /usr/share/miniconda || true
-      - name: add some paths to PATH
-        run:  |
-          echo "$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: 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 "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 "KRAKEN_DEFAULT_DB  $kraken_dir" >> config/settings.conf
-          make
-          make test
-
-
+            multiqc fastqc bowtie2 perl-gd perl-gdgraph salmid staramr kalamari taxonkit