def _get_manifest_dir(data=None, name=None):
"""
get manifest directory from the data dictionary, falling back on alternatives
it prefers, in order:
1. locating it from the bcbio_system.yaml file
2. locating it from the galaxy directory
3. location it from the python executable.
it can accept either the data or config dictionary
"""
manifest_dir = None
if data:
bcbio_system = tz.get_in(["config", "bcbio_system"], data, None)
bcbio_system = bcbio_system if bcbio_system else data.get("bcbio_system", None)
if bcbio_system:
sibling_dir = os.path.normpath(os.path.dirname(bcbio_system))
else:
sibling_dir = dd.get_galaxy_dir(data)
if sibling_dir:
manifest_dir = os.path.normpath(os.path.join(sibling_dir, os.pardir,
"manifest"))
if not manifest_dir or not os.path.exists(manifest_dir):
manifest_dir = os.path.join(config_utils.get_base_installdir(), "manifest")
if not os.path.exists(manifest_dir) and name:
manifest_dir = os.path.join(config_utils.get_base_installdir(name), "manifest")
return manifest_dir
def _get_manifest_dir(data=None, name=None):
"""
get manifest directory from the data dictionary, falling back on alternatives
it prefers, in order:
1. locating it from the bcbio_system.yaml file
2. locating it from the galaxy directory
3. location it from the python executable.
it can accept either the data or config dictionary
"""
manifest_dir = None
if data:
bcbio_system = tz.get_in(["config", "bcbio_system"], data, None)
bcbio_system = bcbio_system if bcbio_system else data.get(
"bcbio_system", None)
if bcbio_system:
sibling_dir = os.path.normpath(os.path.dirname(bcbio_system))
else:
sibling_dir = dd.get_galaxy_dir(data)
if sibling_dir:
manifest_dir = os.path.normpath(
os.path.join(sibling_dir, os.pardir, "manifest"))
if not manifest_dir or not os.path.exists(manifest_dir):
manifest_dir = os.path.join(config_utils.get_base_installdir(),
"manifest")
if not os.path.exists(manifest_dir) and name:
manifest_dir = os.path.join(config_utils.get_base_installdir(name),
"manifest")
return manifest_dir
def _get_versions_manifest():
"""Retrieve versions from a pre-existing manifest of installed software.
"""
all_pkgs = ["htseq", "cn.mops", "vt", "platypus-variant", "gatk-framework"] + \
[p.get("name", p["cmd"]) for p in _cl_progs] + [p["name"] for p in _alt_progs]
manifest_dir = os.path.join(config_utils.get_base_installdir(), "manifest")
if os.path.exists(manifest_dir):
out = []
for plist in ["toolplus", "brew", "python", "r", "debian", "custom"]:
pkg_file = os.path.join(manifest_dir, "%s-packages.yaml" % plist)
if os.path.exists(pkg_file):
with open(pkg_file) as in_handle:
pkg_info = yaml.safe_load(in_handle)
added = []
for pkg in all_pkgs:
if pkg in pkg_info:
added.append(pkg)
out.append({
"program": pkg,
"version": pkg_info[pkg]["version"]
})
for x in added:
all_pkgs.remove(x)
out.sort(key=lambda x: x["program"])
for pkg in all_pkgs:
out.append({"program": pkg, "version": ""})
return out
def _get_versions_manifest():
"""Retrieve versions from a pre-existing manifest of installed software.
"""
all_pkgs = ["htseq", "cn.mops", "vt", "platypus-variant", "gatk-framework"] + \
[p.get("name", p["cmd"]) for p in _cl_progs] + [p["name"] for p in _alt_progs]
manifest_dir = os.path.join(config_utils.get_base_installdir(), "manifest")
if os.path.exists(manifest_dir):
out = []
for plist in ["toolplus", "brew", "python", "r", "debian", "custom"]:
pkg_file = os.path.join(manifest_dir, "%s-packages.yaml" % plist)
if os.path.exists(pkg_file):
with open(pkg_file) as in_handle:
pkg_info = yaml.safe_load(in_handle)
added = []
for pkg in all_pkgs:
if pkg in pkg_info:
added.append(pkg)
out.append({"program": pkg, "version": pkg_info[pkg]["version"]})
for x in added:
all_pkgs.remove(x)
out.sort(key=lambda x: x["program"])
for pkg in all_pkgs:
out.append({"program": pkg, "version": ""})
return out