unit-testing.yml

on: 
  push:
    branches: [master, dev, esearch-input]
name: Pull-down-all-accessions

jobs:
  build:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: ['ubuntu-20.04' ]
        perl: [ '5.32' ]
        runner_id: [0, 1]
    name: chunk ${{ matrix.runner_id }} 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@v2
        with:
          path: Kalamari

      - name: apt-get install
        run:  sudo apt-get install ca-certificates tree
        
      - name: install-edirect
        run:  |
          sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)"
          echo $HOME/edirect >> $GITHUB_PATH
          echo $GITHUB_WORKSPACE/Kalamari/bin >> $GITHUB_PATH
          tree $HOME/edirect
      - name: check-env
        run:  echo "$PATH"
      - name: download
        run: |
          runner_id=${{ matrix.runner_id }}
          echo "Runner_id is $runner_id"
          # Make a chunk input spreadsheet by just adding
          # each sample to chromosomes.tsv
          head -n 1 Kalamari/src/chromosomes.tsv > header.tsv
          tail -n +2 Kalamari/src/plasmids.tsv    >  in.tsv
          tail -n +2 Kalamari/src/chromosomes.tsv >> in.tsv

          total_lines=$(wc -l < in.tsv)
          start_line=$(( $runner_id * $total_lines / 2 + 1 ))
          end_line=$(( ($runner_id + 1) * $total_lines / 2 -1 ))
          echo "($runner_id) start_line: $start_line"
          echo "($runner_id) end_line: $end_line"
          cat header.tsv > chunk_${runner_id}.tsv
          sed -n "${start_line},${end_line}p" in.tsv >> chunk_${runner_id}.tsv
          perl Kalamari/bin/downloadKalamari.pl --numcpus 1 --outdir kalamari.out --buffersize 100 chunk_${runner_id}.tsv
      - name: check-results
        run:  tree kalamari.out
      - name: check-file-sizes
        run:  |
          find kalamari.out -name '*.fasta.gz' > fasta.sizes
          #cat fasta.sizes | xargs -n 100 ls -lhS