unit-testing.Yersinia.Kraken2.yml

# This is a subsampling unit test to get early results
on: 
  push:
    branches: [master, dev, validate-taxonomy]
name: Genera-with-Kraken2

env:
  TSV: "Kalamari/src/genus.tsv"
  DB: "kraken2"
  SRC_CHR: "Kalamari/src/chromosomes.tsv"
  SRC_PLD: "Kalamari/src/plasmids.tsv"
  GENUS: Yersinia

jobs:
  build:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: ['ubuntu-20.04' ]
        perl: [ '5.32' ]
        GENUS: [ 'Yersinia', 'Listeria']
    name: ${{ matrix.GENUS }} Perl ${{ matrix.perl }} on ${{ matrix.os }}
    steps:
      - name: Set up perl
        uses: shogo82148/actions-setup-perl@v1
        with:
          perl-version: ${{ matrix.perl }}
          multi-thread: "true"
      - name: checkout my repo
        uses: actions/checkout@v4
        with:
          path: Kalamari

      - name: env check
        run:  |
          echo $PATH | tr ':' '\n' | sort
      - name: apt-get install
        run:  sudo apt-get install ca-certificates tree jellyfish ncbi-entrez-direct
      - name: select for only for this genus
        run:  |
          head -n 1 ${{ env.SRC_CHR }} > ${{ env.TSV }}
          grep -m 2 ${{ matrix.GENUS }} ${{ env.SRC_CHR }} >> ${{ env.TSV }}
          grep -m 2 ${{ matrix.GENUS }} ${{ env.SRC_PLD }} >> ${{ env.TSV }}
          echo "These are the ${{ matrix.GENUS }} genomes for downstream tests"
          column -ts $'\t' ${{ env.TSV }}
          hexdump -c ${{ env.TSV }}
      - name: download
        run:  |
          perl Kalamari/bin/downloadKalamari.pl --outdir ${{ matrix.GENUS }} ${{ env.TSV }}
          find ${{ matrix.GENUS }} -name '*.fasta.gz' | xargs gunzip -v
      - name: check-results
        run:  |
          tree ${{ matrix.GENUS }}
          echo "First two lines of each fasta file:"
          find ${{ matrix.GENUS }} -name '*.fasta' | xargs head -n 2 | cut -c 1-60
      - name: install kraken
        run:  |
          wget https://github.com/DerrickWood/kraken2/archive/refs/tags/v2.1.2.tar.gz -O kraken-v2.1.2.tar.gz
          tar zxvf kraken-v2.1.2.tar.gz
          cd kraken2-2.1.2 && bash install_kraken2.sh target && cd -
          ls -lhS kraken2-2.1.2/target
          chmod +x kraken2-2.1.2/target/*
      - name: build taxonomy
        run: |
          export PATH=$PATH:Kalamari/bin
          buildTaxonomy.sh
          ls -lh Kalamari/share
      - name: Kraken2 database
        run:  |
          export PATH=$PATH:kraken2-2.1.2/target
          which kraken2-build
          mkdir -pv ${{ env.DB }}
          cp -rv Kalamari/share/kalamari-*/taxonomy ${{ env.DB }}/taxonomy
          find ${{ matrix.GENUS }} -name '*.fasta' -exec kraken2-build --db ${{ env.DB }} --add-to-library {} \;
          tree ${{ env.DB }}
          echo ".....Building the database....."
          kraken2-build --build --db ${{ env.DB }} --threads 2
      - name: Kraken2 view results
        run:  |
          export PATH=$PATH:kraken2-2.1.2/target
          tree ${{ env.DB }}
          ls -lhSR ${{ env.DB }}
          QUERY=$(find ${{ matrix.GENUS }} -name '*.fasta' | head -n 1)
          echo "QUERY is $QUERY"
          set -x; kraken2 --db ${{ env.DB }} --report kraken2.report --use-mpa-style --output kraken2.raw $QUERY; set +x;
          head kraken2.report kraken2.raw