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
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
