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Linux bioconda

Linux bioconda #1876

Workflow file for this run

name: Linux bioconda
on:
workflow_dispatch:
schedule:
- cron: '15 3 * * *' # 3:15am everyday
repository_dispatch:
types: [linux-bioconda-test, install-test]
jobs:
conda_linux_x86_64:
runs-on: ubuntu-latest
steps:
- name: When was this run
run: date
- name: configure conda
run: |
. $CONDA/bin/activate
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
- name: install AMRFinderPlus
run: |
. $CONDA/bin/activate
conda install --update-deps -c conda-forge -c bioconda -y ncbi-amrfinderplus
amrfinder --version
- name: download latest AMRFinderPlus database
run: |
source /usr/share/miniconda/bin/activate
echo CONDA_PREFIX = ${CONDA_PREFIX}
/usr/share/miniconda/bin/amrfinder --force_update
- name: Software and DB version
run: |
source /usr/share/miniconda/bin/activate
amrfinder --database_version
- name: download tests
run: |
BASE_URL=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/master
curl --silent -L \
-O ${BASE_URL}/test_dna.fa \
-O ${BASE_URL}/test_prot.fa \
-O ${BASE_URL}/test_prot.gff \
-O ${BASE_URL}/test_both.expected \
-O ${BASE_URL}/test_dna.expected \
-O ${BASE_URL}/test_dna_mut_all.expected \
-O ${BASE_URL}/test_prot.expected \
-O ${BASE_URL}/test_amrfinder.sh
- name: run tests
run: |
source /usr/share/miniconda/bin/activate
echo CONDA_PREFIX = $CONDA_PREFIX
bash ./test_amrfinder.sh path
conda_linux_aarch64:
runs-on: ubuntu-24.04-arm
steps:
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
- name: When was this run
run: date
- name: configure conda
shell: bash -el {0}
run: |
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
- name: install AMRFinderPlus
shell: bash -el {0}
run: |
conda install --update-deps -c conda-forge -c bioconda -y ncbi-amrfinderplus
amrfinder --version
- name: download latest AMRFinderPlus database
shell: bash -el {0}
run: amrfinder --force_update
- name: Software and DB version
shell: bash -el {0}
run: amrfinder --database_version
- name: download tests
run: |
BASE_URL=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/master
curl --silent -L \
-O ${BASE_URL}/test_dna.fa \
-O ${BASE_URL}/test_prot.fa \
-O ${BASE_URL}/test_prot.gff \
-O ${BASE_URL}/test_both.expected \
-O ${BASE_URL}/test_dna.expected \
-O ${BASE_URL}/test_dna_mut_all.expected \
-O ${BASE_URL}/test_prot.expected \
-O ${BASE_URL}/test_amrfinder.sh
- name: run tests
shell: bash -el {0}
run: bash ./test_amrfinder.sh path