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fix release build script #642

fix release build script

fix release build script #642

Workflow file for this run

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