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(): 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()