makefile.yml

name: compile and e.coli

on:
  push:
    paths:
    - '**.sm'
    - '**.py'
    - '**.sh'
    - 'src/*'
    - '.github/workflows/*.yml'
    branches-ignore:
    - v2

  pull_request:
    branches: [ master ]

jobs:
  build_linux:
    name:    Linux
    runs-on: ubuntu-latest
    steps:
    - name: Checkout
      uses: actions/checkout@v3

    - name: Install Rust
      uses: actions-rs/toolchain@v1
      with:
        toolchain: stable

    - name: Setup Python 3.11
      uses: actions/setup-python@v2
      with:
        python-version: 3.11

    - name: Install Conda
      uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        mamba-version: "*"
        channels: conda-forge,bioconda
        python-version: 3.11
        
    - name: Install dependencies
      run: |
        sudo apt-get update
        mamba install -c conda-forge -c bioconda 'python=3.11' 'pulp<=2.7.0' 'snakemake-minimal>7,<8' GraphAligner mashmap winnowmap
        sudo apt-get install libcurl4-openssl-dev
        pip install networkx

        echo ""
        echo "CONDA LIST"
        echo ""
        conda list

        echo ""
        echo "PYTHON TEST"
        echo "  "`command -v python`
        echo "  "`python --version`

        echo  > x.py "from importlib import metadata"
        echo >> x.py "for dist in metadata.distributions():"
        echo >> x.py "  print(dist._path)"
        python x.py

        echo  > x.py "from importlib.metadata import version"
        echo >> x.py "version('networkx')"
        python x.py

        echo  > x.py "import networkx as nx"
        echo >> x.py "G = nx.Graph()"
        echo >> x.py "print(G)"
        python x.py

    - name: Compile
      run: |
        cd src
        make -j 2

    - name: Fetch Data
      run: |
        curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_hifi_subset24x.fastq.gz -o hifi.fastq.gz
        curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_ont_subset50x.fastq.gz  -o ont.fastq.gz
        curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli-test-cache.tar          -o cache.tar
        tar -xf cache.tar

    - name: Assemble
      run: |
        reportLogs() {
          for fn in `find . -name \*err -print` ; do
            echo ""
            echo "==BEGIN $fn"
            cat $fn
            echo "==END   $fn"
          done
          exit 1
        }
        export PATH=${PATH}:$CONDA/bin

        rm -f mbg.sh
        rm -f ga.sh
        rm -f lib/verkko/bin/utgcns

        echo  > mbg.sh '#!/bin/sh'
        echo >> mbg.sh 'xz -dc ../../cache/hifi-resolved.gfa.xz  > hifi-resolved.gfa'
        echo >> mbg.sh 'cp     ../../cache/hifi_nodecov.csv        hifi_nodecov.csv'
        echo >> mbg.sh 'xz -dc ../../cache/paths.gaf.xz          > paths.gaf'

        echo  > ga.sh '#!/bin/sh'
        echo >> ga.sh 'if [ ! -e "graph.index" ] ; then'
        echo >> ga.sh '  touch graph.index'
        echo >> ga.sh '  touch diploid.index'
        echo >> ga.sh '  touch empty.gaf'
        echo >> ga.sh 'else'
        echo >> ga.sh '  xz -dc ../../cache/aligned001.WORKING.gaf.xz > aligned001.WORKING.gaf'
        echo >> ga.sh 'fi'

        echo  > lib/verkko/bin/utgcns '#!/bin/sh'
        echo >> lib/verkko/bin/utgcns 'if [ ! -e part001.fasta ]; then'
        echo >> lib/verkko/bin/utgcns 'cp ../../cache/part001.fasta packages/part001.fasta.WORKING'
        echo >> lib/verkko/bin/utgcns 'fi'
        echo >> lib/verkko/bin/utgcns ''
        echo >> lib/verkko/bin/utgcns 'if [ ! -e part002.fasta ]; then'
        echo >> lib/verkko/bin/utgcns 'cp ../../cache/part002.fasta packages/part002.fasta.WORKING'
        echo >> lib/verkko/bin/utgcns 'fi'
        
        chmod 755 mbg.sh
        chmod 755 ga.sh
        chmod 755 lib/verkko/bin/utgcns

        ./bin/verkko -d asm --mbg $PWD/mbg.sh --graphaligner $PWD/ga.sh --hifi ./hifi.fastq.gz --nano ./ont.fastq.gz
        if [ ! -s asm/assembly.fasta ]; then
           reportLogs
        fi