def check_git():
try:
version = _subprocess.check_output(['git', '--version'])
except OSError:
print('Dependency error: git not found.')
print('Please install git version 2.4 or more recent to continue')
version = version.rstrip().split(' ')[-1].split('.')
version_A, version_B, version_C = map(int, version)
if not (version_A >= 2 and version_B >= 4):
print('Dependency warning: git version < 2.4')
print('''Proceeding but if git-related issues encountered,
try updating git to version 2.4 or more recent''')
else:
print('git %s found: ok' % '.'.join(version))
def check_git():
try:
version = _subprocess.check_output(['git','--version'])
except OSError:
print('Dependency error: git not found.')
print('Please install git version 2.4 or more recent to continue')
version = version.rstrip().split(' ')[-1].split('.')
version_A, version_B, version_C = map(int, version)
if not (version_A >= 2 and version_B >= 4):
print('Dependency warning: git version < 2.4')
print('''Proceeding but if git-related issues encountered,
try updating git to version 2.4 or more recent''')
else:
print('git %s found: ok' % '.'.join(version))
def check_no_error(path='',
system=False,
java_commands=False,
extra=False,
extra_pre=False,
success_returncode=1):
'''
check a binary executable can be called.
A failure is considered as OSError, not a non-zero exit status.
Can check in default baga location or a specified path or the system path
or java.
Additional commands and be appended with 'extra' list or pre-pended with
'extra-pre' list e.g., specifying 'python2' for when python3 defaults but
python >3.3 is installed but not supported.
'''
if java_commands:
p = _subprocess.Popen(['java'] + java_commands,
stdout=_subprocess.PIPE,
stderr=_subprocess.STDOUT)
output = p.stdout.read()
if 'Error:' in output:
print(output)
return (False)
else:
print(output)
return (True)
else:
if system:
cmd = path[-1:]
elif path[0][0] == _os.path.sep or path[0] == '':
# absolute path to elsewhere provided
cmd = [_os.path.sep.join(path)]
else:
cmd = [_os.path.sep.join(['external_programs'] + path)]
if extra:
cmd += extra
if extra_pre:
cmd = extra_pre + cmd
try:
o = _subprocess.check_output(cmd)
o = '\n'.join(['external> ' + l for l in o.split('\n')]) + '\n'
print(o) # eventually put in the debugging log <== too much noise
# some programs output a help screen if commands not given
# . . . they are installed and available
return (True)
except _subprocess.CalledProcessError as e:
if e.returncode == success_returncode:
# some programs that exit return non-zero code if commands not given
# usually this is 1, but occasionally it is 2 (e.g. cutadapt)
# but a fail on 2 is e.g. python calling a non-existent python program
# should be set in the dependencies dictionary if not 1 (default)
# . . . but they are installed and available
return (True)
else:
return (False)
except OSError as e:
print('{}: {}'.format(cmd[0], e))
return (False)
def check_no_error(path = '',
system = False,
java_commands = False,
extra = False,
extra_pre = False,
success_returncode = 1):
'''
check a binary executable can be called.
A failure is considered as OSError, not a non-zero exit status.
Can check in default baga location or a specified path or the system path
or java.
Additional commands and be appended with 'extra' list or pre-pended with
'extra-pre' list e.g., specifying 'python2' for when python3 defaults but
python >3.3 is installed but not supported.
'''
if java_commands:
p = _subprocess.Popen(['java'] + java_commands, stdout=_subprocess.PIPE, stderr=_subprocess.STDOUT)
output = p.stdout.read()
if 'Error:' in output:
print(output)
return(False)
else:
print(output)
return(True)
else:
if system:
cmd = path[-1:]
elif path[0][0] == _os.path.sep or path[0] == '':
# absolute path to elsewhere provided
cmd = [_os.path.sep.join(path)]
else:
cmd = [_os.path.sep.join(['external_programs'] + path)]
if extra:
cmd += extra
if extra_pre:
cmd = extra_pre + cmd
try:
o = _subprocess.check_output(cmd)
o = '\n'.join(['external> '+l for l in o.split('\n')])+'\n'
print(o) # eventually put in the debugging log <== too much noise
# some programs output a help screen if commands not given
# . . . they are installed and available
return(True)
except _subprocess.CalledProcessError as e:
if e.returncode == success_returncode:
# some programs that exit return non-zero code if commands not given
# usually this is 1, but occasionally it is 2 (e.g. cutadapt)
# but a fail on 2 is e.g. python calling a non-existent python program
# should be set in the dependencies dictionary if not 1 (default)
# . . . but they are installed and available
return(True)
else:
return(False)
except OSError as e:
print('{}: {}'.format(cmd[0], e))
return(False)
