bring back rest of CI

.github/workflows/unittests.yml

@@ -102,4 +102,97 @@ jobs:
         with:
           repository: lskatz/CG-Pipeline
           path: CG-Pipeline
-          ref:  v0.5
+          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
+          buildTaxonomy.sh
+          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
+
+