fix release build script #642
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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 |