def test_install():
exit_now = False
print ("Checking the various dependencies")
print ("--------------------------------------------")
if test_suite.which(jellyfish_path):
print ("Using jellyfish in " + test_suite.which(jellyfish_path))
a = subprocess.check_output([jellyfish_path, "--version"])
if len(a) < 11:
print ("Unable to automatically determine jellyfish version. Ensure that it is version 2.0.0 or greater")
else:
if a[10] != "2":
print (
"Jellyfish version does not seem to be greater than 2.0.0. Please ensure that it is version 2.0.0 or greater, continuing run..."
)
else:
print ("ERROR: Jellyfish not found. Set variable jellyfish_path correctly")
exit_now = True
if test_suite.which(gpmetis_path):
print ("Using GPMETIS in " + test_suite.which(gpmetis_path))
else:
print ("ERROR: GPMETIS not found in path. Set variable gpmetis_path correctly")
exit_now = True
try:
import cvxopt
except ImportError, e:
print ("ERROR: CVXOPT not installed into Python. Please see online manual for instructions.")
exit_now = True
def test_install_kallisto():
if test_suite.which(kallisto_path):
print('Using Kallisto in ') + test_suite.which(kallisto_path)
return True
else:
print('ERROR: Kallisto not found in path ' + test_suite.which(kallisto_path))
print('Kallisto filtering DISABLED.')
return False
def test_install_gnu_parallel():
if test_suite.which(gnu_parallel_path):
print('Using GNU Parallel in ') + test_suite.which(gnu_parallel_path)
else:
print(
'ERROR: GNU Parallel not found in path. If you need to run multi-threaded, GNU Parallel is needed. Set variable gnu_parallel_path correctly'
)
exit_now = True
def test_install_quorum():
if test_suite.which(quorum_path):
print('Using Quorum in ') + test_suite.which(quorum_path)
else:
print(
'ERROR: Quorum not found in path. Set variable quorum_path correctly'
)
sys.exit()
def test_install_gnu_parallel():
if test_suite.which(gnu_parallel_path):
print ("Using GNU Parallel in ") + test_suite.which(gnu_parallel_path)
else:
print (
"ERROR: GNU Parallel not found in path. If you need to run multi-threaded, GNU Parallel is needed. Set variable gnu_parallel_path correctly"
)
exit_now = True
def test_install_kallisto():
if test_suite.which(kallisto_path):
print('Using Kallisto in ') + test_suite.which(kallisto_path)
return True
else:
print('ERROR: Kallisto not found in path ' + test_suite.which(kallisto_path))
print('Kallisto filtering DISABLED.')
return False
def test_install():
exit_now = False;
print('Checking the various dependencies')
print('--------------------------------------------')
if test_suite.which(jellyfish_path):
print('Using jellyfish in ' + test_suite.which(jellyfish_path))
a=subprocess.check_output([jellyfish_path,'--version'])
if len(a) < 11:
print('Unable to automatically determine jellyfish version. Ensure that it is version 2.0.0 or greater')
else:
if a[10] != '2':
print('Jellyfish version does not seem to be greater than 2.0.0. Please ensure that it is version 2.0.0 or greater, continuing run...')
else:
print('ERROR: Jellyfish not found. Set variable jellyfish_path correctly'); exit_now = True
if test_suite.which(gpmetis_path):
print('Using GPMETIS in ' + test_suite.which(gpmetis_path))
else:
print('ERROR: GPMETIS not found in path. Set variable gpmetis_path correctly'); exit_now = True
try:
import cvxopt
except ImportError, e:
print('ERROR: CVXOPT not installed into Python. Please see online manual for instructions.'); exit_now = True
def test_install_quorum():
if test_suite.which(quorum_path):
print('Using Quorum in ') + test_suite.which(quorum_path)
else:
print('ERROR: Quorum not found in path. Set variable quorum_path correctly');
sys.exit()
