def compile_aligner(logger, only_clean=False):
global contig_aligner
default_requirements = ['nucmer', 'delta-filter', 'show-coords', 'show-snps', 'mummer', 'mummerplot', 'mgaps']
if only_clean:
aligners_to_try = [
('E-MEM', 'emem', default_requirements + ['e-mem']),
('MUMmer', 'mummer', default_requirements)]
for i, (name, flag_name, requirements) in enumerate(aligners_to_try):
compile_tool(name, contig_aligner_dirpath, requirements, logger=logger, only_clean=only_clean, flag_suffix='.' + flag_name)
return True
mummer_failed = check_prev_compilation_failed('MUMmer', mummer_failed_compilation_flag, just_notice=True, logger=logger)
emem_failed = check_prev_compilation_failed('E-MEM', e_mem_failed_compilation_flag, just_notice=True, logger=logger)
if mummer_failed and emem_failed:
contig_aligner = None
logger.error("Compilation of contig aligner software was unsuccessful! QUAST functionality will be limited.")
return False
if contig_aligner is not None:
compilation_failed = emem_failed if is_emem_aligner() else mummer_failed
if not compilation_failed:
return True
contig_aligner = None
if not qconfig.force_nucmer and not emem_failed:
if get_installed_emem() or isfile(join(contig_aligner_dirpath, 'e-mem')):
emem_requirements = default_requirements
elif qconfig.platform_name == 'macosx' and isfile(join(contig_aligner_dirpath, 'e-mem-osx')):
shutil.copy(join(contig_aligner_dirpath, 'e-mem-osx'), join(contig_aligner_dirpath, 'e-mem'))
emem_requirements = default_requirements
else:
emem_requirements = default_requirements + ['e-mem']
aligners_to_try = [
('E-MEM', 'emem', emem_requirements),
('MUMmer', 'mummer', default_requirements)]
else:
aligners_to_try = [
('MUMmer', 'mummer', default_requirements)]
for i, (name, flag_name, requirements) in enumerate(aligners_to_try):
success_compilation = compile_tool(name, contig_aligner_dirpath, requirements, just_notice=(i < len(aligners_to_try) - 1),
logger=logger, only_clean=only_clean, flag_suffix='.' + flag_name,
make_cmd='no-emem' if 'e-mem' not in requirements else None)
if not success_compilation:
continue
contig_aligner = name # successfully compiled
return True
logger.error("Compilation of contig aligner software was unsuccessful! QUAST functionality will be limited.")
return False
def compile_aligner(logger, only_clean=False, compile_all_aligners=False):
global contig_aligner
global contig_aligner_dirpath
if not compile_all_aligners:
if contig_aligner_dirpath is not None and not \
check_prev_compilation_failed(contig_aligner, join(contig_aligner_dirpath, 'make.failed'), just_notice=True, logger=logger):
return True
if not qconfig.force_nucmer and not contig_aligner_dirpath and qconfig.platform_name == 'macosx':
if get_installed_emem() or \
not check_prev_compilation_failed('E-MEM', e_mem_failed_compilation_flag, just_notice=True, logger=logger):
contig_aligner = 'E-MEM'
contig_aligner_dirpath = join(qconfig.LIBS_LOCATION, 'E-MEM-osx')
return True
default_requirements = ['nucmer', 'delta-filter', 'show-coords', 'show-snps', 'mummer', 'mgaps']
if qconfig.platform_name == 'macosx':
aligners_to_try = [
('MUMmer', join(qconfig.LIBS_LOCATION, 'MUMmer3.23-osx'), default_requirements)]
else:
if not qconfig.force_nucmer:
if get_installed_emem():
emem_requirements = default_requirements
else:
emem_requirements = default_requirements + ['e-mem']
aligners_to_try = [
('E-MEM', join(qconfig.LIBS_LOCATION, 'E-MEM-linux'), emem_requirements),
('MUMmer', join(qconfig.LIBS_LOCATION, 'MUMmer3.23-linux'), default_requirements)]
else:
aligners_to_try = [
('MUMmer', join(qconfig.LIBS_LOCATION, 'MUMmer3.23-linux'), default_requirements)]
for i, (name, dirpath, requirements) in enumerate(aligners_to_try):
success_compilation = compile_tool(name, dirpath, requirements, just_notice=(i < len(aligners_to_try) - 1),
logger=logger, only_clean=only_clean, make_cmd='no-emem' if 'E-MEM' in name and get_installed_emem() else None)
if not success_compilation:
continue
contig_aligner = name
contig_aligner_dirpath = dirpath # successfully compiled
if not compile_all_aligners:
return True
if compile_all_aligners and contig_aligner and contig_aligner_dirpath:
return True
logger.error("Compilation of contig aligner software was unsuccessful! QUAST functionality will be limited.")
return False
def compile_aligner(logger, only_clean=False):
requirements = ['minimap2']
aligner_failed_compilation_flag = join(contig_aligner_dirpath,
'make.failed')
if only_clean:
compile_tool('Minimap2',
contig_aligner_dirpath,
requirements,
logger=logger,
only_clean=only_clean)
return True
if check_prev_compilation_failed('Minimap2',
aligner_failed_compilation_flag,
just_notice=True,
logger=logger):
logger.error(
"Compilation of contig aligner software was unsuccessful! QUAST functionality will be limited."
)
return False
if compile_tool('Minimap2',
contig_aligner_dirpath,
requirements,
just_notice=False,
logger=logger,
only_clean=only_clean):
return True
logger.error(
"Compilation of contig aligner software was unsuccessful! QUAST functionality will be limited."
)
return False
def download_tool(tool,
tool_version,
required_files,
logger,
url,
only_clean=False):
tool_dirpath = get_dir_for_download(tool + tool_version,
tool,
required_files,
logger,
only_clean=only_clean)
if not tool_dirpath:
return None
if only_clean:
if os.path.isdir(tool_dirpath):
shutil.rmtree(tool_dirpath, ignore_errors=True)
return tool_dirpath
failed_compilation_flag = join(tool_dirpath, 'make.failed')
if not all(os.path.exists(join(tool_dirpath, fpath)) for fpath in required_files) and not \
check_prev_compilation_failed(tool, failed_compilation_flag):
downloaded_fpath = join(tool_dirpath, tool + '.tar.gz')
logger.main_info(' Downloading third-party tools...')
download_unpack_compressed_tar(tool, url, downloaded_fpath,
tool_dirpath, logger)
if not all(
os.path.exists(join(tool_dirpath, fpath))
for fpath in required_files):
logger.warning('Failed to download ' + tool + ' from ' + url +
'and unpack it into ' + tool_dirpath)
return None
return tool_dirpath
def download_manta(logger, bed_fpath=None, only_clean=False):
global manta_dirpath
manta_dirpath = get_dir_for_download('manta' + manta_version,
'Manta', [config_manta_relpath],
logger,
only_clean=only_clean)
if not manta_dirpath:
return False
manta_build_dirpath = join(manta_dirpath, 'build')
config_manta_fpath = get_manta_fpath()
if only_clean:
if os.path.isdir(manta_build_dirpath):
shutil.rmtree(manta_build_dirpath, ignore_errors=True)
return True
if not qconfig.no_sv and bed_fpath is None and not isfile(
config_manta_fpath):
if qconfig.platform_name == 'linux_64':
url = manta_linux_url
fpath = manta_ext_linux_fpath
elif qconfig.platform_name == 'macosx':
url = manta_osx_url
fpath = manta_ext_osx_fpath
else:
logger.warning('Manta is not available for your platform.')
return False
if not exists(manta_build_dirpath):
os.makedirs(manta_build_dirpath)
manta_downloaded_fpath = join(manta_build_dirpath, 'manta.tar.bz2')
if isfile(fpath):
logger.info('Copying manta from ' + fpath)
shutil.copy(fpath, manta_downloaded_fpath)
logger.info('Unpacking ' + manta_downloaded_fpath + ' into ' +
manta_build_dirpath)
unpack_tar(manta_downloaded_fpath, manta_build_dirpath)
else:
failed_compilation_flag = join(manta_dirpath, 'make.failed')
if check_prev_compilation_failed('Manta', failed_compilation_flag):
print_manta_warning(logger)
return False
logger.main_info(' Downloading binary distribution of Manta...')
download_unpack_tar_bz('Manta', url, manta_downloaded_fpath,
manta_build_dirpath, logger)
manta_demo_dirpath = join(manta_build_dirpath, 'share', 'demo')
if os.path.isdir(manta_demo_dirpath):
shutil.rmtree(manta_demo_dirpath, ignore_errors=True)
if not isfile(config_manta_fpath):
logger.warning(
'Failed to download binary distribution from https://github.com/ablab/quast/external_tools/manta '
'and unpack it into ' + join(manta_dirpath, 'build/'))
print_manta_warning(logger)
return False
return True
def compile_gnuplot(logger, only_clean=False):
tool_dirpath = join(qconfig.LIBS_LOCATION, 'gnuplot')
tool_exec_fpath = gnuplot_exec_fpath()
if only_clean:
if isfile(tool_exec_fpath):
os.remove(tool_exec_fpath)
return True
if not isfile(tool_exec_fpath):
failed_compilation_flag = join(tool_dirpath, 'make.failed')
if check_prev_compilation_failed('gnuplot',
failed_compilation_flag,
just_notice=True,
logger=logger):
return None
logger.main_info("Compiling gnuplot...")
prev_dir = os.getcwd()
os.chdir(tool_dirpath)
return_code = qutils.call_subprocess(
[
'./configure', '--with-qt=no', '--disable-wxwidgets',
'--prefix=' + tool_dirpath
],
stdout=open(join(tool_dirpath, 'make.log'), 'w'),
stderr=open(join(tool_dirpath, 'make.err'), 'w'),
indent=' ')
if return_code == 0:
return_code = qutils.call_subprocess(
['make'],
stdout=open(join(tool_dirpath, 'make.log'), 'w'),
stderr=open(join(tool_dirpath, 'make.err'), 'w'),
indent=' ')
os.chdir(prev_dir)
if return_code != 0 or not isfile(tool_exec_fpath):
write_failed_compilation_flag('gnuplot',
tool_dirpath,
failed_compilation_flag,
just_notice=True,
logger=logger)
return None
return tool_exec_fpath
def compile_aligner(logger, only_clean=False):
requirements = ['nucmer', 'delta-filter', 'show-coords', 'show-snps', 'mummer', 'mummerplot', 'mgaps']
mummer_failed_compilation_flag = join(contig_aligner_dirpath, 'make.failed')
if only_clean:
compile_tool('MUMmer', contig_aligner_dirpath, requirements, logger=logger, only_clean=only_clean)
return True
if check_prev_compilation_failed('MUMmer', mummer_failed_compilation_flag, just_notice=True, logger=logger):
logger.error("Compilation of contig aligner software was unsuccessful! QUAST functionality will be limited.")
return False
fix_configure_timestamps(contig_aligner_dirpath)
prefix_arg = '--prefix=' + contig_aligner_dirpath
if compile_tool('MUMmer', contig_aligner_dirpath, requirements, just_notice=False, logger=logger, only_clean=only_clean,
configure_args=[prefix_arg, 'LDFLAGS=-static'] if qconfig.platform_name != 'macosx' else [prefix_arg]):
return True
logger.error("Compilation of contig aligner software was unsuccessful! QUAST functionality will be limited.")
return False
def download_manta(logger, bed_fpath=None, only_clean=False):
if only_clean:
if os.path.isdir(manta_build_dirpath):
shutil.rmtree(manta_build_dirpath)
return True
if not qconfig.no_sv and bed_fpath is None and not isfile(config_manta_fpath):
if qconfig.platform_name == 'linux_64':
url = manta_linux_url
fpath = manta_ext_linux_fpath
elif qconfig.platform_name == 'macosx':
url = manta_osx_url
fpath = manta_ext_osx_fpath
else:
logger.warning('Manta is not available for your platform.')
return False
if not exists(manta_build_dirpath):
os.makedirs(manta_build_dirpath)
manta_downloaded_fpath = join(manta_build_dirpath, 'manta.tar.bz2')
if isfile(fpath):
logger.info('Copying manta from ' + fpath)
shutil.copy(fpath, manta_downloaded_fpath)
logger.info('Unpacking ' + manta_downloaded_fpath + ' into ' + manta_build_dirpath)
unpack_tar(manta_downloaded_fpath, manta_build_dirpath)
else:
failed_compilation_flag = join(manta_dirpath, 'make.failed')
if check_prev_compilation_failed('Manta', failed_compilation_flag):
print_manta_warning(logger)
return True
logger.main_info(' Downloading binary distribution of Manta...')
download_unpack_tar_bz('Manta', url, manta_downloaded_fpath, manta_build_dirpath, logger)
if not isfile(config_manta_fpath):
logger.warning('Failed to download binary distribution from https://github.com/ablab/quast/external_tools/manta '
'and unpack it into ' + join(manta_dirpath, 'build/'))
print_manta_warning(logger)
return True
def download_tool(tool, tool_version, required_files, logger, url, only_clean=False):
tool_dirpath = get_dir_for_download(tool + tool_version, tool, required_files, logger, only_clean=only_clean)
if not tool_dirpath:
return None
if only_clean:
if os.path.isdir(tool_dirpath):
shutil.rmtree(tool_dirpath, ignore_errors=True)
return tool_dirpath
failed_compilation_flag = join(tool_dirpath, 'make.failed')
if not all(os.path.exists(join(tool_dirpath, fpath)) for fpath in required_files) and not \
check_prev_compilation_failed(tool, failed_compilation_flag):
downloaded_fpath = join(tool_dirpath, tool + '.tar.gz')
logger.main_info(' Downloading ' + tool + '...')
download_unpack_compressed_tar(tool, url, downloaded_fpath, tool_dirpath, logger)
if not all(os.path.exists(join(tool_dirpath, fpath)) for fpath in required_files):
logger.warning('Failed to download ' + tool + ' from ' + url + 'and unpack it into ' + tool_dirpath)
return None
return tool_dirpath
def manta_compilation_failed():
failed_compilation_flag = join(manta_dirpath, 'make.failed')
if check_prev_compilation_failed('Manta', failed_compilation_flag):
return True
return False
def manta_compilation_failed():
failed_compilation_flag = join(manta_dirpath, 'make.failed')
if check_prev_compilation_failed('Manta', failed_compilation_flag):
return True
return False
def compile_jellyfish(logger, only_clean=False):
make_logs_basepath = join(jellyfish_src_dirpath, 'make')
failed_compilation_flag = make_logs_basepath + '.failed'
if only_clean:
safe_rm(jellyfish_bin_fpath)
safe_rm(failed_compilation_flag)
return True
if exists(jellyfish_bin_fpath):
try:
import jellyfish
except:
safe_rm(jellyfish_bin_fpath)
if not exists(jellyfish_bin_fpath):
if check_prev_compilation_failed('Jellyfish',
failed_compilation_flag,
logger=logger):
return False
# making
logger.main_info('Compiling Jellyfish (details are in ' +
make_logs_basepath + '.log and make.err)')
os.utime(join(jellyfish_src_dirpath, 'aclocal.m4'), None)
os.utime(join(jellyfish_src_dirpath, 'Makefile.in'), None)
os.utime(join(jellyfish_src_dirpath, 'config.h.in'), None)
os.utime(join(jellyfish_src_dirpath, 'configure'), None)
prev_dir = os.getcwd()
os.chdir(jellyfish_src_dirpath)
safe_rm(
join(jellyfish_src_dirpath, 'swig', 'python', '__init__.pyc')
) ## in case if jellyfish was compiled with different python version
safe_rm(jellyfish_python_dirpath)
call_subprocess([
'./configure', '--prefix=' + jellyfish_dirpath,
'--enable-python-binding=' + jellyfish_python_dirpath,
'PYTHON_VERSION=' + str(sys.version_info[0]) + '.' +
str(sys.version_info[1])
],
stdout=open(make_logs_basepath + '.log', 'w'),
stderr=open(make_logs_basepath + '.err', 'w'))
try:
return_code = call_subprocess(
['make'],
stdout=open(make_logs_basepath + '.log', 'a'),
stderr=open(make_logs_basepath + '.err', 'a'),
logger=logger)
return_code = call_subprocess(
['make', 'install'],
stdout=open(make_logs_basepath + '.log', 'a'),
stderr=open(make_logs_basepath + '.err', 'a'),
logger=logger)
except IOError:
os.chdir(prev_dir)
msg = 'Permission denied accessing ' + jellyfish_src_dirpath + '. Did you forget sudo?'
logger.notice(msg)
return False
os.chdir(prev_dir)
if return_code != 0 or not exists(jellyfish_bin_fpath):
write_failed_compilation_flag('Jellyfish',
jellyfish_src_dirpath,
failed_compilation_flag,
logger=logger)
return False
return True