def test_experiment_data(tmpdir, bioc_fetch): bioconductor_skeleton.write_recipe('Affyhgu133A2Expr', str(tmpdir), config, recursive=False, packages=bioc_fetch) meta = utils.load_first_metadata(str(tmpdir.join('bioconductor-affyhgu133a2expr'))).meta assert any(dep.startswith('curl ') for dep in meta['requirements']['run']) assert len(meta['source']['url']) == 3 assert not tmpdir.join('bioconductor-affyhgu133a2expr', 'build.sh').exists() assert tmpdir.join('bioconductor-affyhgu133a2expr', 'post-link.sh').exists() assert tmpdir.join('bioconductor-affyhgu133a2expr', 'pre-unlink.sh').exists()
def test_experiment_data(tmpdir, bioc_fetch): bioconductor_skeleton.write_recipe('affydata', str(tmpdir), config, recursive=False, packages=bioc_fetch) meta = utils.load_first_metadata(str(tmpdir.join('bioconductor-affydata'))).meta assert any(dep.startswith('curl ') for dep in meta['requirements']['run']) assert len(meta['source']['url']) == 3 assert not tmpdir.join('bioconductor-affydata', 'build.sh').exists() assert tmpdir.join('bioconductor-affydata', 'post-link.sh').exists() assert tmpdir.join('bioconductor-affydata', 'pre-unlink.sh').exists()
def test_experiment_data(tmpdir): bioconductor_skeleton.write_recipe('affydata', str(tmpdir), config, recursive=True) meta = utils.load_first_metadata(str( tmpdir.join('bioconductor-affydata'))).meta assert 'wget' in meta['requirements']['run'] assert len(meta['source']['url']) == 3 assert not tmpdir.join('bioconductor-affydata', 'build.sh').exists() assert tmpdir.join('bioconductor-affydata', 'post-link.sh').exists() assert tmpdir.join('bioconductor-affydata', 'pre-unlink.sh').exists()
def test_annotation_data(tmpdir, bioc_fetch): bioconductor_skeleton.write_recipe('AHCytoBands', str(tmpdir), config, recursive=False, packages=bioc_fetch) meta = utils.load_first_metadata( str(tmpdir.join('bioconductor-ahcytobands'))).meta assert 'wget' in meta['requirements']['run'] assert len(meta['source']['url']) == 3 assert not tmpdir.join('bioconductor-ahcytobands', 'build.sh').exists() assert tmpdir.join('bioconductor-ahcytobands', 'post-link.sh').exists() assert tmpdir.join('bioconductor-ahcytobands', 'pre-unlink.sh').exists()
def test_meta_contents(tmpdir, bioc_fetch): config = { 'channels': ['conda-forge', 'bioconda', 'defaults'] } bioconductor_skeleton.write_recipe( 'edgeR', recipe_dir=str(tmpdir), config=config, recursive=False, packages=bioc_fetch) edger_meta = utils.load_first_metadata(str(tmpdir.join('bioconductor-edger'))).meta assert 'r-rcpp' in edger_meta['requirements']['run'] # The rendered meta has {{ compiler('c') }} filled in, so we need to check # for one of those filled-in values. names = [i.split()[0] for i in edger_meta['requirements']['build']] assert 'libstdcxx-ng' in names or 'clang_osx-64' in names # bioconductor, bioarchive, and cargoport assert len(edger_meta['source']['url']) == 3