Update src/scripts/get_layout_from_mbg.py #777
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 | |
| miniforge-version: latest | |
| use-mamba: true | |
| 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 samtools seqtk | |
| sudo apt-get install gcc-11 g++-11 libcurl4-openssl-dev liblzma-dev libbz2-dev bamtools libbamtools-dev | |
| pip install networkx pysam | |
| sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-11 100 | |
| sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-11 100 | |
| 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 | |
| echo "" | |
| echo "BAMTOOLS TEST" | |
| echo " "`command -v bamtools` | |
| - 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 'samtools dict ../../cache/part001.fasta | samtools view -b -S > packages/part001.bam00000002.bam' | |
| 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 'samtools dict ../../cache/part002.fasta | samtools view -b -S > packages/part002.bam00000001.bam' | |
| 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 |