def cli(ctx, **kwds):
"""Make a bioconda recipe, given a R or bioconductor package name.
package_name = motifbreakR
bioconda_dir = '/Users/nturaga/Documents/workspace'.
"""
package_name = kwds.get("package_name")
clone = kwds.get("clone")
update = kwds.get("update")
bioconda_dir_path = kwds.get("bioconda_dir_path")
write_bioconda_recipe(package_name, clone, update, bioconda_dir_path)
return
def cli(ctx, **kwds):
"""Make a bioconda recipe, given a R or bioconductor package name.
package_name = motifbreakR
bioconda_dir = '/Users/nturaga/Documents/workspace'.
"""
package_name = kwds.get("package_name")
clone = kwds.get("clone")
update = kwds.get("update")
bioconda_dir_path = kwds.get("bioconda_dir_path")
write_bioconda_recipe(package_name, clone, update, bioconda_dir_path)
return
def __init__(self, requirement, bioconda_path=None, update=False):
"""Initialize Requirements class for Bioc tool builder."""
parts = requirement.split("@", 1)
# Get version from requirements, if version not given
if len(parts) > 1:
name = parts[0]
version = "@".join(parts[1:])
else:
name = parts[0]
version = None
if name == "R":
self.name = name
self.version = version
else:
# Write biconda recipe with given requirement
if bioconda_path is None:
bioconda_path = os.path.expanduser("~")
write_bioconda_recipe(name, True, update, bioconda_path)
recipe_path = os.path.join(bioconda_path,
"bioconda-recipes",
"recipes",
"bioconductor-" + name.lower(),
"meta.yaml")
if not os.path.exists(recipe_path):
recipe_path = os.path.join(bioconda_path,
"bioconda-recipes",
"recipes",
"r-" + name.lower(),
"meta.yaml")
with open(recipe_path, 'r') as f:
doc = yaml.safe_load(f)
if not version:
version = doc["package"]["version"]
package_url = doc["about"]["home"]
package_help = doc["about"]["summary"]
self.name = name
self.version = version
self.package_url = package_url
self.package_help = package_help