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small update in the cache ontologies and update in all of them #113

small update in the cache ontologies and update in all of them

small update in the cache ontologies and update in all of them #113

Workflow file for this run

name: Conda Build
on: [push, pull_request]
jobs:
build:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v2
- name: Set up Miniconda
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
python-version: 3.8
channels: conda-forge,defaults,bioconda
- name: Create conda environment
run: conda env create -f environment.yml
- name: Activate conda environment
run: |
source $CONDA/etc/profile.d/conda.sh
conda activate sdrf-pipelines
shell: bash
- name: Install conda-build
run: |
source $CONDA/etc/profile.d/conda.sh
conda activate sdrf-pipelines
conda install -n sdrf-pipelines conda-build anaconda-client
shell: bash -l {0}
- name: Activate conda environment and build package
run: |
source $CONDA/etc/profile.d/conda.sh
conda activate sdrf-pipelines
conda build recipe
PACKAGE_PATH=$(find /usr/share/miniconda/envs/sdrf-pipelines/conda-bld/noarch/ -name "sdrf-pipelines-*.tar.bz2" | head -n 1)
conda install --offline "$PACKAGE_PATH"
shell: bash -l {0}
- name: Test the installed package
run: |
conda activate sdrf-pipelines
parse_sdrf --help
shell: bash -l {0}
- name: Test validation of SDRF file
run: |
conda activate sdrf-pipelines
parse_sdrf validate-sdrf --sdrf_file tests/data/reference/PDC000126/PDC000126.sdrf.tsv
shell: bash -l {0}
- name: Test validation of SDRF file with cache only
run: |
conda activate sdrf-pipelines
parse_sdrf validate-sdrf --sdrf_file tests/data/reference/PDC000126/PDC000126.sdrf.tsv --use_ols_cache_only
shell: bash -l {0}