remove bashism #654
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| 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 |