diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 4dbf4f51..5e767cb3 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -21,13 +21,21 @@ jobs: - name: Install dependencies run: | sudo apt update && sudo apt install -y --no-install-recommends \ - curl wget unzip + curl wget unzip git \ + autoconf automake libtool build-essential gawk pkg-config \ + python3-pip + pip3 install scikit-learn kaggle + wget https://raw.githubusercontent.com/binpash/pash/main/scripts/up.sh + sh up.sh + export PASH_TOP="$PWD/pash/" - name: Set execute permissions for main.sh run: chmod +x main.sh - name: Run Benchmark for ${{ matrix.benchmark }} - run: ./main.sh ${{ matrix.benchmark }} --small + run: | + export PASH_TOP="$PWD/pash/" + "$PASH_TOP/pa.sh" -c "./main.sh ${{ matrix.benchmark }} --small" - name: Upload .out and .err files uses: actions/upload-artifact@v4 diff --git a/Dockerfile b/Dockerfile index 0ca86bac..ef16c8d9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,16 +10,43 @@ RUN apt update && apt install -y --no-install-recommends \ curl \ wget \ unzip \ + git \ samtools \ minimap2 \ bcftools \ python3-pip \ vim \ - ffmpeg unrtf imagemagick libarchive-tools libncurses5-dev libncursesw5-dev zstd liblzma-dev libbz2-dev zip unzip nodejs tcpdump \ - git + ffmpeg \ + unrtf \ + imagemagick \ + libarchive-tools \ + libncurses5-dev \ + libncursesw5-dev \ + zstd \ + liblzma-dev \ + libbz2-dev \ + zip \ + unzip \ + nodejs \ + tcpdump \ + autoconf \ + automake \ + libtool \ + build-essential \ + gawk \ + pkg-config RUN pip3 install --break-system-packages \ scikit-learn \ kaggle +# Install PaSh +RUN wget https://raw.githubusercontent.com/binpash/pash/main/scripts/up.sh && \ + sh up.sh && \ + export PASH_TOP="$PWD/pash/" + +# Test PaSh installation +RUN "$PWD/pash/pa.sh" -c "echo hi" + +# Default command CMD ["bash"]