def prep_simple_make(path=False, configure=False, alt_command=False):
if path:
_os.chdir(_os.path.sep.join(path))
if configure:
_subprocess.call(['./configure'])
if alt_command:
_subprocess.call([alt_command])
else:
_subprocess.call(['make'])
if path:
_os.chdir(_os.path.sep.join([_os.path.pardir] * len(path)))
def prep_simple_make(path = False, configure = False, alt_command = False):
if path:
_os.chdir(_os.path.sep.join(path))
if configure:
_subprocess.call(['./configure'])
if alt_command:
_subprocess.call([alt_command])
else:
_subprocess.call(['make'])
if path:
_os.chdir(_os.path.sep.join([_os.path.pardir]*len(path)))
def get_git(name, description, source, url, commit, checksum, destination,
preparation, checker):
'''
Get a dependency from git
'''
if _os.path.realpath(_os.path.curdir) != destination:
try:
_os.chdir(destination)
except OSError:
_os.makedirs(destination)
_os.chdir(destination)
try:
# clear any previous verions
_shutil.rmtree(url.split('/')[-1].replace('.git', ''))
except OSError:
pass
git_server = url.replace('https://', '').replace('http://',
'').split('/')[0]
print('Downloading {} via git from {} . . .'.format(name, git_server))
_subprocess.call(['git', 'clone', url])
_os.chdir(url.split('/')[-1].replace('.git', ''))
_subprocess.call(['git', 'checkout', commit])
# if repo uses git submodules, those will be set to the correct revisions for this commit
# else will do nothing
_subprocess.call(['git', 'submodule', 'update', '--init'])
working_dir = _os.path.sep.join(
[destination, url.split('/')[-1].replace('.git', '')])
if preparation is not None:
for do_this in preparation:
if isinstance(do_this['arguments'], dict):
do_this['function'](**do_this['arguments'])
else:
do_this['function'](*do_this['arguments'])
# restore position in path if a prepare changed it
if working_dir != _os.path.realpath(_os.path.curdir):
_os.chdir(working_dir)
_os.chdir(_os.path.pardir)
_os.chdir(_os.path.pardir)
def get_download(name, description, source, url, commit, checksum, destination,
preparation, checker):
'''
Download and unpack a dependancy
'''
##
initialdir = _os.path.abspath(_os.curdir)
try:
_os.chdir(destination)
except OSError:
_os.makedirs(destination)
_os.chdir(destination)
if checksum:
hasher_algorithm = checksum.split('=')[0]
if hasher_algorithm == 'md5':
hasher = _hashlib.md5()
elif hasher_algorithm == 'sha1':
hasher = _hashlib.sha1()
elif hasher_algorithm == 'sha224':
hasher = _hashlib.sha224()
elif hasher_algorithm == 'sha256':
hasher = _hashlib.sha256()
elif hasher_algorithm == 'sha384':
hasher = _hashlib.sha384()
elif hasher_algorithm == 'sha512':
hasher = _hashlib.sha512()
else:
print("{} checksums not implemented in Python's hashlib!".format(
hasher_algorithm))
print('Downloading: %s' % url)
req = _urllib2.urlopen(url)
CHUNK = 16 * 1024 * 16
data = _cStringIO.StringIO()
c = 0
for chunk in iter(lambda: req.read(CHUNK), ''):
c += CHUNK
print("{:,} bytes".format(c))
data.write(chunk)
print('Download complete . . .')
data.seek(0)
if checksum:
buff = data.read(65536)
while len(buff) > 0:
hasher.update(buff)
buff = data.read(65536)
e = '. . . checksum fail!'
assert hasher.hexdigest() == checksum.split('=')[1], e
print('. . . checksum passed!')
data.seek(0)
if url[-6:] == 'tar.gz':
archive = _tarfile.open(mode="r:gz", fileobj=data)
elif url[-7:] == 'tar.bz2':
archive = _tarfile.open(mode="r:bz2", fileobj=data)
elif url[-4:] == '.zip':
archive = _zipfile.ZipFile(data)
if destination == 'local_packages':
# extract as a pypi python package
release = url.split('/')[-1][:-7]
print('Extracting {} to {}'.format(
release, _os.path.sep.join([destination, name])))
c = 0
nostrip = {'pysam'}
if name in nostrip:
try:
_shutil.rmtree(archive.getnames()[0])
except OSError:
pass
#_shutil.rmtree(_os.path.sep.join([destination, archive.getnames()[0]]))
# some python modules should not be stripped . . more complex install
for member in archive.getmembers():
if member.isreg():
archive.extract(member)
print(member.name)
c += 1
else:
# others don't need additional compilation
check_path1 = '{}/{}'.format(release, name)
for member in archive.getmembers():
if member.isreg() and check_path1 in member.name:
member.name = _os.path.sep.join(
member.name.split(_os.path.sep)[1:])
archive.extract(member)
c += 1
print('Extracted {} files'.format(c))
else:
# extract as a generic external program
archive.extractall()
if preparation:
for do_this in preparation:
if 'just_packages' in do_this['arguments']:
# this is the only thing that differentiates this prepare()
# from others that need some chdir <== this should be improved
# see dep dict
curdir = _os.path.abspath(_os.curdir)
_os.chdir(_os.path.pardir)
do_this['function'](*do_this['arguments']['package_list'])
# return to previous folder
_os.chdir(curdir)
else:
extracted_base_dir = archive.getnames()[0].split(
_os.path.sep)[0]
curdir = _os.path.abspath(_os.curdir)
# go to installed folder
_os.chdir(_os.path.sep.join([destination, extracted_base_dir]))
do_this['function'](**do_this['arguments'])
# return to previous folder
_os.chdir(curdir)
_os.chdir(initialdir)
def get_download(name, description, source, url, commit, checksum, destination, preparation, checker):
'''
Download and unpack a dependancy
'''
##
initialdir = _os.path.abspath(_os.curdir)
try:
_os.chdir(destination)
except OSError:
_os.makedirs(destination)
_os.chdir(destination)
if checksum:
hasher_algorithm = checksum.split('=')[0]
if hasher_algorithm == 'md5':
hasher = _hashlib.md5()
elif hasher_algorithm == 'sha1':
hasher = _hashlib.sha1()
elif hasher_algorithm == 'sha224':
hasher = _hashlib.sha224()
elif hasher_algorithm == 'sha256':
hasher = _hashlib.sha256()
elif hasher_algorithm == 'sha384':
hasher = _hashlib.sha384()
elif hasher_algorithm == 'sha512':
hasher = _hashlib.sha512()
else:
print("{} checksums not implemented in Python's hashlib!".format(hasher_algorithm))
print('Downloading: %s' % url)
req = _urllib2.urlopen(url)
CHUNK = 16 * 1024 * 16
data = _cStringIO.StringIO()
c = 0
for chunk in iter(lambda: req.read(CHUNK), ''):
c += CHUNK
print("{:,} bytes".format(c))
data.write(chunk)
print('Download complete . . .')
data.seek(0)
if checksum:
buff = data.read(65536)
while len(buff) > 0:
hasher.update(buff)
buff = data.read(65536)
e = '. . . checksum fail!'
assert hasher.hexdigest() == checksum.split('=')[1], e
print('. . . checksum passed!')
data.seek(0)
if url[-6:] == 'tar.gz':
archive = _tarfile.open(mode="r:gz", fileobj = data)
elif url[-7:] == 'tar.bz2':
archive = _tarfile.open(mode="r:bz2", fileobj = data)
elif url[-4:] == '.zip':
archive = _zipfile.ZipFile(data)
if destination == 'local_packages':
# extract as a pypi python package
release = url.split('/')[-1][:-7]
print('Extracting {} to {}'.format(release, _os.path.sep.join([destination,name])))
c = 0
nostrip = {'pysam'}
if name in nostrip:
try:
_shutil.rmtree(archive.getnames()[0])
except OSError:
pass
#_shutil.rmtree(_os.path.sep.join([destination, archive.getnames()[0]]))
# some python modules should not be stripped . . more complex install
for member in archive.getmembers():
if member.isreg():
archive.extract(member)
print(member.name)
c += 1
else:
# others don't need additional compilation
check_path1 = '{}/{}'.format(release,name)
for member in archive.getmembers():
if member.isreg() and check_path1 in member.name:
member.name = _os.path.sep.join(member.name.split(_os.path.sep)[1:])
archive.extract(member)
c += 1
print('Extracted {} files'.format(c))
else:
# extract as a generic external program
archive.extractall()
if preparation:
for do_this in preparation:
if 'just_packages' in do_this['arguments']:
# this is the only thing that differentiates this prepare()
# from others that need some chdir <== this should be improved
# see dep dict
curdir = _os.path.abspath(_os.curdir)
_os.chdir(_os.path.pardir)
do_this['function'](*do_this['arguments']['package_list'])
# return to previous folder
_os.chdir(curdir)
else:
extracted_base_dir = archive.getnames()[0].split(_os.path.sep)[0]
curdir = _os.path.abspath(_os.curdir)
# go to installed folder
_os.chdir(_os.path.sep.join([destination,extracted_base_dir]))
do_this['function'](**do_this['arguments'])
# return to previous folder
_os.chdir(curdir)
_os.chdir(initialdir)
def get_git(name, description, source, url, commit, checksum, destination, preparation, checker):
'''
Get a dependency from git
'''
if _os.path.realpath(_os.path.curdir) != destination:
try:
_os.chdir(destination)
except OSError:
_os.makedirs(destination)
_os.chdir(destination)
try:
# clear any previous verions
_shutil.rmtree(url.split('/')[-1].replace('.git',''))
except OSError:
pass
git_server = url.replace('https://','').replace('http://','').split('/')[0]
print('Downloading {} via git from {} . . .'.format(name, git_server))
_subprocess.call(['git', 'clone', url])
_os.chdir(url.split('/')[-1].replace('.git',''))
_subprocess.call(['git', 'checkout', commit])
# if repo uses git submodules, those will be set to the correct revisions for this commit
# else will do nothing
_subprocess.call(['git', 'submodule', 'update', '--init'])
working_dir = _os.path.sep.join([destination,url.split('/')[-1].replace('.git','')])
if preparation is not None:
for do_this in preparation:
if isinstance(do_this['arguments'], dict):
do_this['function'](**do_this['arguments'])
else:
do_this['function'](*do_this['arguments'])
# restore position in path if a prepare changed it
if working_dir != _os.path.realpath(_os.path.curdir):
_os.chdir(working_dir)
_os.chdir(_os.path.pardir)
_os.chdir(_os.path.pardir)
