Skip to content

Workflow file for this run

name: Build and test mapping coverage
on:
push:
branches: [ master ]
paths-ignore:
- '**/*.md'
pull_request:
branches: [ master ]
paths-ignore:
- '**/*.md'
env:
# Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
BUILD_TYPE: DEBUG
jobs:
linux:
# The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
# You can convert this to a matrix build if you need cross-platform coverage.
# See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-20.04]
compiler:
- { compiler: GNU, CC: gcc-11, CXX: g++-11 }
steps:
- name: Cancel Workflow Action
uses: styfle/[email protected]
- name: Checkout
uses: actions/checkout@v2
with:
submodules: 'true'
- name: Setup apt
run:
- sudo apt install build-essential manpages-dev software-properties-common

Check failure on line 38 in .github/workflows/build-and-test.yml

View workflow run for this annotation

GitHub Actions / Build and test mapping coverage

Invalid workflow file

The workflow is not valid. .github/workflows/build-and-test.yml (Line: 38, Col: 9): A sequence was not expected
- sudo add-apt-repository ppa:ubuntu-toolchain-r/test
- sudo apt update && sudo apt install
- name: Install Requirements
run: sudo apt install -y
${{ matrix.compiler.CC }}
${{ matrix.compiler.CXX }}
libhts-dev
libjemalloc-dev
libgsl-dev
zlib1g-dev
libhts-dev
samtools
bedtools
- name: Build
env:
CC: ${{ matrix.compiler.CC }}
CXX: ${{ matrix.compiler.CXX }}
# Build your program with the given configuration
run: cmake -H. -Bbuild -DCMAKE_BUILD_TYPE=${BUILD_TYPE} && cmake --build build --
- name: Basic version test
env:
CC: ${{ matrix.compiler.CC }}
CXX: ${{ matrix.compiler.CXX }}
run: build/bin/mashmap -v
- name: Test coverage
env:
CC: ${{ matrix.compiler.CC }}
CXX: ${{ matrix.compiler.CXX }}
run: |
ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/mashmap \
-r data/scerevisiae8.fa.gz
-q data/scerevisiae8.fa.gz
--pi 95 -n 1 -Y '#'
-o scerevisiae8.paf;
scripts/test.sh data/scerevisiae8.fa.gz.fai scerevisiae8.paf 0.92