def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
qiime_config = load_qiime_config()
rdp_jarpath = get_rdp_jarpath()
if rdp_jarpath == None:
rdp_version = "Not installed."
else:
rdp_version = split(rdp_jarpath)[1]
java_version = get_java_version()
if java_version is None:
java_version = "Not installed."
system_info = [
("Platform", platform),
("Python version",python_version.replace('\n', ' ')),
("Python executable",executable)]
max_len = max([len(e[0]) for e in system_info])
print "\nSystem information"
print "=================="
for v in system_info:
print "%*s:\t%s" % (max_len,v[0],v[1])
version_info = [
("PyCogent version", pycogent_lib_version),
("NumPy version", numpy_lib_version),
("matplotlib version", matplotlib_lib_version),
("biom-format version", biom_lib_version),
("qcli version", qcli_lib_version),
("QIIME library version", get_qiime_library_version()),
("QIIME script version", __version__),
("PyNAST version (if installed)", pynast_lib_version),
("RDP Classifier version (if installed)", rdp_version),
("Java version (if installed)", java_version),
("Emperor version", emperor_lib_version)]
max_len = max([len(e[0]) for e in version_info])
print "\nDependency versions"
print "==================="
for v in version_info:
print "%*s:\t%s" % (max_len,v[0],v[1])
print "\nQIIME config values"
print "==================="
max_len = max([len(key) for key in qiime_config])
for key,value in qiime_config.items():
print "%*s:\t%s"%(max_len,key,value)
#run the Testcase.main function to do the tests
# need to mess with the arg string, otherwise TestCase complains
if (opts.test):
print "\n\nrunning checks:\n"
test_main(argv=["","-v"])
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if opts.haiku:
print "QIIME provides insight\nmicrobial in nature\nto ecology"
exit(0)
qiime_config = load_qiime_config()
test = opts.test
qiime_base_install = opts.qiime_base_install
rdp_jarpath = get_rdp_jarpath()
if rdp_jarpath is None:
rdp_version = "Not installed."
else:
rdp_version = split(rdp_jarpath)[1]
java_version = get_java_version()
if java_version is None:
java_version = "Not installed."
system_info = [
("Platform", platform),
("Python version", python_version.replace('\n', ' ')),
("Python executable", executable)]
max_len = max([len(e[0]) for e in system_info])
print "\nSystem information"
print "=================="
for v in system_info:
print "%*s:\t%s" % (max_len, v[0], v[1])
version_info = [
("PyCogent version", pycogent_lib_version),
("NumPy version", numpy_lib_version),
("SciPy version", scipy_lib_version),
("matplotlib version", matplotlib_lib_version),
("biom-format version", biom_lib_version),
("qcli version", qcli_lib_version),
("pyqi version", pyqi_lib_version),
("scikit-bio version", skbio_lib_version),
("QIIME library version", get_qiime_library_version()),
("QIIME script version", __version__),
("PyNAST version (if installed)", pynast_lib_version),
("Emperor version", emperor_lib_version)]
if not qiime_base_install:
version_info += [
("RDP Classifier version (if installed)", rdp_version),
("Java version (if installed)", java_version)]
max_len = max([len(e[0]) for e in version_info])
print "\nDependency versions"
print "==================="
for v in version_info:
print "%*s:\t%s" % (max_len, v[0], v[1])
print "\nQIIME config values"
print "==================="
max_len = max([len(key) for key in qiime_config])
for key, value in qiime_config.items():
print "%*s:\t%s" % (max_len, key, value)
if test:
if qiime_base_install:
suite = TestLoader().loadTestsFromTestCase(QIIMEDependencyBase)
else:
suite = TestLoader().loadTestsFromTestCase(QIIMEDependencyFull)
if opts.verbose:
verbosity = 2
else:
verbosity = 1
TextTestRunner(stream=stdout, verbosity=verbosity).run(suite)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if opts.haiku:
print "QIIME provides insight\nmicrobial in nature\nto ecology"
exit(0)
qiime_config = load_qiime_config()
test = opts.test
qiime_base_install = opts.qiime_base_install
rdp_jarpath = get_rdp_jarpath()
if rdp_jarpath is None:
rdp_version = "Not installed."
else:
rdp_version = split(rdp_jarpath)[1]
java_version = get_java_version()
if java_version is None:
java_version = "Not installed."
system_info = [("Platform", platform),
("Python version", python_version.replace('\n', ' ')),
("Python executable", executable)]
max_len = max([len(e[0]) for e in system_info])
print "\nSystem information"
print "=================="
for v in system_info:
print "%*s:\t%s" % (max_len, v[0], v[1])
version_info = [("NumPy version", numpy_lib_version),
("SciPy version", scipy_lib_version),
("matplotlib version", matplotlib_lib_version),
("biom-format version", biom_lib_version),
("qcli version", qcli_lib_version),
("pyqi version", pyqi_lib_version),
("scikit-bio version", skbio_lib_version),
("QIIME library version", get_qiime_library_version()),
("QIIME script version", __version__),
("PyNAST version (if installed)", pynast_lib_version),
("Emperor version", emperor_lib_version)]
if not qiime_base_install:
version_info += [("RDP Classifier version (if installed)",
rdp_version),
("Java version (if installed)", java_version)]
max_len = max([len(e[0]) for e in version_info])
print "\nDependency versions"
print "==================="
for v in version_info:
print "%*s:\t%s" % (max_len, v[0], v[1])
print "\nQIIME config values"
print "==================="
max_len = max([len(key) for key in qiime_config])
for key, value in qiime_config.items():
print "%*s:\t%s" % (max_len, key, value)
if test:
if qiime_base_install:
suite = TestLoader().loadTestsFromTestCase(QIIMEDependencyBase)
else:
suite = TestLoader().loadTestsFromTestCase(QIIMEDependencyFull)
if opts.verbose:
verbosity = 2
else:
verbosity = 1
TextTestRunner(stream=stdout, verbosity=verbosity).run(suite)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if opts.haiku:
print "QIIME provides insight\nmicrobial in nature\nto ecology"
exit(0)
qiime_config = load_qiime_config()
test = opts.test
qiime_full_install = opts.qiime_full_install
rdp_jarpath = get_rdp_jarpath()
if rdp_jarpath is None:
rdp_version = "Not installed."
else:
rdp_version = split(rdp_jarpath)[1]
java_version = get_java_version()
if java_version is None:
java_version = "Not installed."
system_info = [("Platform", platform),
("Python version", python_version.replace('\n', ' ')),
("Python executable", executable)]
max_len = max([len(e[0]) for e in system_info])
print "\nSystem information"
print "=================="
for v in system_info:
print "%*s:\t%s" % (max_len, v[0], v[1])
print "\nQIIME default reference information"
print "==================================="
print "For details on what files are used as QIIME's default references, see here:"
print " https://github.com/biocore/qiime-default-reference/releases/tag/%s" % qdr_lib_version
version_info = [("QIIME library version", get_qiime_library_version()),
("QIIME script version", __version__),
("qiime-default-reference version", qdr_lib_version),
("NumPy version", numpy_lib_version),
("SciPy version", scipy_lib_version),
("pandas version", pandas_lib_version),
("matplotlib version", matplotlib_lib_version),
("biom-format version", biom_lib_version),
("h5py version", h5py_lib_version),
("qcli version", qcli_lib_version),
("pyqi version", pyqi_lib_version),
("scikit-bio version", skbio_lib_version),
("PyNAST version", pynast_lib_version),
("Emperor version", emperor_lib_version),
("burrito version", burrito_lib_version),
("burrito-fillings version", bfillings_lib_version),
("sortmerna version", sortmerna_lib_version),
("sumaclust version", sumaclust_lib_version),
("swarm version", swarm_lib_version),
("gdata", gdata_installed)]
if qiime_full_install:
version_info += [("RDP Classifier version (if installed)",
rdp_version),
("Java version (if installed)", java_version)]
max_len = max([len(e[0]) for e in version_info])
print "\nDependency versions"
print "==================="
for v in version_info:
print "%*s:\t%s" % (max_len, v[0], v[1])
print "\nQIIME config values"
print "==================="
print "For definitions of these settings and to learn how to configure QIIME, see here:"
print " http://qiime.org/install/qiime_config.html"
print " http://qiime.org/tutorials/parallel_qiime.html\n"
max_len = max([len(key) for key in qiime_config])
for key, value in qiime_config.items():
print "%*s:\t%s" % (max_len, key, value)
if test:
if qiime_full_install:
print "\nQIIME full install test results"
print "==============================="
suite = TestLoader().loadTestsFromTestCase(QIIMEDependencyFull)
else:
print "\nQIIME base install test results"
print "==============================="
suite = TestLoader().loadTestsFromTestCase(QIIMEDependencyBase)
if opts.verbose:
verbosity = 2
else:
verbosity = 1
TextTestRunner(stream=stdout, verbosity=verbosity).run(suite)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if opts.haiku:
print "QIIME provides insight\nmicrobial in nature\nto ecology"
exit(0)
qiime_config = load_qiime_config()
test = opts.test
qiime_full_install = opts.qiime_full_install
rdp_jarpath = get_rdp_jarpath()
if rdp_jarpath is None:
rdp_version = "Not installed."
else:
rdp_version = split(rdp_jarpath)[1]
java_version = get_java_version()
if java_version is None:
java_version = "Not installed."
system_info = [
("Platform", platform),
("Python version", python_version.replace('\n', ' ')),
("Python executable", executable)]
max_len = max([len(e[0]) for e in system_info])
print "\nSystem information"
print "=================="
for v in system_info:
print "%*s:\t%s" % (max_len, v[0], v[1])
print "\nQIIME default reference information"
print "==================================="
print "For details on what files are used as QIIME's default references, see here:"
print " https://github.com/biocore/qiime-default-reference/releases/tag/%s" % qdr_lib_version
version_info = [
("QIIME library version", get_qiime_library_version()),
("QIIME script version", __version__),
("qiime-default-reference version", qdr_lib_version),
("NumPy version", numpy_lib_version),
("SciPy version", scipy_lib_version),
("pandas version", pandas_lib_version),
("matplotlib version", matplotlib_lib_version),
("biom-format version", biom_lib_version),
("h5py version", h5py_lib_version),
("qcli version", qcli_lib_version),
("pyqi version", pyqi_lib_version),
("scikit-bio version", skbio_lib_version),
("PyNAST version", pynast_lib_version),
("Emperor version", emperor_lib_version),
("burrito version", burrito_lib_version),
("burrito-fillings version", bfillings_lib_version),
("sortmerna version", sortmerna_lib_version),
("sumaclust version", sumaclust_lib_version),
("swarm version", swarm_lib_version),
("gdata", gdata_installed)
]
if qiime_full_install:
version_info += [
("RDP Classifier version (if installed)", rdp_version),
("Java version (if installed)", java_version)]
max_len = max([len(e[0]) for e in version_info])
print "\nDependency versions"
print "==================="
for v in version_info:
print "%*s:\t%s" % (max_len, v[0], v[1])
print "\nQIIME config values"
print "==================="
print "For definitions of these settings and to learn how to configure QIIME, see here:"
print " http://qiime.org/install/qiime_config.html"
print " http://qiime.org/tutorials/parallel_qiime.html\n"
max_len = max([len(key) for key in qiime_config])
for key, value in qiime_config.items():
print "%*s:\t%s" % (max_len, key, value)
if test:
if qiime_full_install:
print "\nQIIME full install test results"
print "==============================="
suite = TestLoader().loadTestsFromTestCase(QIIMEDependencyFull)
else:
print "\nQIIME base install test results"
print "==============================="
suite = TestLoader().loadTestsFromTestCase(QIIMEDependencyBase)
if opts.verbose:
verbosity = 2
else:
verbosity = 1
TextTestRunner(stream=stdout, verbosity=verbosity).run(suite)
