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ci: update how we append to PATH in actions #11

ci: update how we append to PATH in actions

ci: update how we append to PATH in actions #11

Workflow file for this run

name: CI
on: [push, pull_request]
jobs:
build:
runs-on: ubuntu-latest
steps:
- name: Checkout code
uses: actions/checkout@v4
- name: Setup tmate session
uses: mxschmitt/action-tmate@v3
with:
detached: true
- name: Install Dependencies
run: |
sudo apt-get update
sudo apt-get install -y libstdc++6 liblzma5 libbz2-1.0 bioperl libncurses5
- name: Add binaries to PATH
run: |
echo "$PWD/bin:$PWD/binaries/noarch:$PWD/binaries/linux" >> $GITHUB_PATH
- name: Check binaries
run: |
! (ldd $PWD/binaries/linux/freebayes | grep 'not found')
! (ldd $PWD/binaries/linux/vcfuniq | grep 'not found')
! (ldd $PWD/binaries/linux/samtools | grep 'not found')
! (ldd $PWD/binaries/linux/bcftools | grep 'not found')
# the check snippy step keeps erroring with /usr/bin/env: ‘perl’: Not a directory so check the perl installation
- name: Check perl installation
run: |
perl --version
which perl
- name: Check snippy versions and configurations
run: |
snippy --version
snippy --check
snippy-core --version
snippy-core --check
- name: Run tests
run: |
make -C test