run docs manually #13
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| name: CI | |
| on: | |
| push: | |
| branches: [ master, dev ] | |
| pull_request: | |
| branches: [ master, dev ] | |
| workflow_dispatch: | |
| jobs: | |
| build-test: | |
| runs-on: ubuntu-latest | |
| env: | |
| NIM_VERSION: stable | |
| HTSLIB_VERSION: 1.22.1 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Cache nimble packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.nimble | |
| key: nimble-${{ runner.os }}-${{ hashFiles('strling.nimble') }} | |
| restore-keys: | | |
| nimble-${{ runner.os }}- | |
| - name: Setup Nim | |
| run: | | |
| curl https://nim-lang.org/choosenim/init.sh -sSf > init.sh | |
| sh init.sh -y | |
| echo "$HOME/.nimble/bin" >> $GITHUB_PATH | |
| - name: Install system build deps | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y build-essential autoconf automake libcurl4-openssl-dev libssl-dev zlib1g-dev libbz2-dev liblzma-dev wget unzip | |
| - name: Build htslib | |
| run: | | |
| wget https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2 | |
| tar xjf htslib-${HTSLIB_VERSION}.tar.bz2 | |
| cd htslib-${HTSLIB_VERSION} | |
| autoheader && autoconf && ./configure --enable-libcurl | |
| make -j 2 | |
| echo "LD_LIBRARY_PATH=$PWD" >> $GITHUB_ENV | |
| - name: Nimble install | |
| run: nimble install -y | |
| - name: Build strling help | |
| run: ./strling -h | |
| - name: Unit tests | |
| run: nimble test -y | |
| integration-e2e: | |
| # Only run end-to-end tests on pushes to master to keep PRs fast | |
| if: github.ref == 'refs/heads/master' | |
| runs-on: ubuntu-latest | |
| needs: build-test | |
| env: | |
| HTSLIB_VERSION: 1.10 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Setup Nim | |
| run: | | |
| curl https://nim-lang.org/choosenim/init.sh -sSf > init.sh | |
| sh init.sh -y | |
| echo "$HOME/.nimble/bin" >> $GITHUB_PATH | |
| - name: Install system build deps | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y build-essential autoconf automake libcurl4-openssl-dev libssl-dev zlib1g-dev libbz2-dev liblzma-dev wget unzip | |
| - name: Build htslib | |
| run: | | |
| wget https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2 | |
| tar xjf htslib-${HTSLIB_VERSION}.tar.bz2 | |
| cd htslib-${HTSLIB_VERSION} | |
| autoheader && autoconf && ./configure --enable-libcurl | |
| make -j 2 | |
| echo "LD_LIBRARY_PATH=$PWD" >> $GITHUB_ENV | |
| - name: Nimble install | |
| run: nimble install -y | |
| - name: Download test data | |
| run: | | |
| mkdir -p run_tests | |
| cd run_tests | |
| wget -O data.zip https://ndownloader.figshare.com/articles/11367851?private_link=207b2a78ddcbdb28781b | |
| unzip data.zip | |
| rm data.zip | |
| wget -O chr4.fa.gz https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr4.fa.gz | |
| gzip -d chr4.fa.gz | |
| - name: End-to-end single sample | |
| run: | | |
| cd run_tests | |
| mkdir -p single | |
| ../strling extract -f chr4.fa -g chr4.fa.str -v CANVAS.chr4-39348425_AAGGG_0_400.bam single/CANVAS.chr4-39348425_AAGGG_0_400.str.bin | |
| ../strling call -v -o single/CANVAS.chr4-39348425_AAGGG_0_400 CANVAS.chr4-39348425_AAGGG_0_400.bam single/CANVAS.chr4-39348425_AAGGG_0_400.str.bin | |
| - name: End-to-end joint samples | |
| run: | | |
| cd run_tests | |
| mkdir -p joint | |
| for i in *.bam; do ../strling extract -f chr4.fa -g chr4.fa.str -v $i joint/$i.str.bin; done | |
| ../strling merge -f chr4.fa -v -o joint/strling joint/*.bin | |
| for i in *.bam; do ../strling call -v -b joint/strling-bounds.txt -o joint/$i $i joint/$i.str.bin; done | |
| - name: Inspect outputs | |
| run: | | |
| cd run_tests | |
| head single/*.txt || true | |
| head joint/strling-bounds.txt || true | |
| head joint/*.txt || true |