for fpath in [
fn
for fn in glob(join(quast_package, 'site_packages', '*', '*.pyc'))
]:
os.remove(fpath)
if cmd_in(['clean']):
if isdir('build'):
shutil.rmtree('build')
if isdir('dist'):
shutil.rmtree('dist')
if isdir(name + '.egg-info'):
shutil.rmtree(name + '.egg-info')
download_manta(logger, only_clean=True)
download_all_blast_binaries(logger, only_clean=True)
download_blastdb(logger, only_clean=True)
logger.info('Done.')
sys.exit()
if cmd_in(['test']):
ret_code = os.system('quast.py --test')
sys.exit(ret_code)
def write_version_py():
version_py = os.path.join(os.path.dirname(__file__), quast_package,
'version.py')
with open('VERSION.txt') as f:
v = f.read().strip().split('\n')[0]
try:
compile_bwa(logger, only_clean=True)
compile_bedtools(logger, only_clean=True)
for fpath in [fn for fn in glob(join(quast_package, '*.pyc'))]: os.remove(fpath)
for fpath in [fn for fn in glob(join(quast_package, 'html_saver', '*.pyc'))]: os.remove(fpath)
for fpath in [fn for fn in glob(join(quast_package, 'site_packages', '*', '*.pyc'))]: os.remove(fpath)
if cmd_in(['clean']):
if isdir('build'):
shutil.rmtree('build')
if isdir('dist'):
shutil.rmtree('dist')
if isdir(name + '.egg-info'):
shutil.rmtree(name + '.egg-info')
download_manta(logger, only_clean=False)
download_all_blast_binaries(logger, only_clean=True)
download_blastdb(logger, only_clean=True)
logger.info('Done.')
sys.exit()
if cmd_in(['test']):
ret_code = os.system('quast.py --test')
sys.exit(ret_code)
def write_version_py():
version_py = os.path.join(os.path.dirname(__file__), quast_package, 'version.py')
with open('VERSION.txt') as f:
v = f.read().strip().split('\n')[0]
try:
for fpath in [
fn
for fn in glob(join(quast_package, 'site_packages', '*', '*.pyc'))
]:
os.remove(fpath)
if cmd_in(['clean']):
if isdir('build'):
shutil.rmtree('build')
if isdir('dist'):
shutil.rmtree('dist')
if isdir(name + '.egg-info'):
shutil.rmtree(name + '.egg-info')
download_manta(logger, only_clean=False)
download_all_blast_binaries(logger, only_clean=True)
download_blastdb(logger, only_clean=True)
logger.info('Done.')
sys.exit()
if cmd_in(['test']):
ret_code = os.system('quast.py --test')
sys.exit(ret_code)
def write_version_py():
version_py = os.path.join(os.path.dirname(__file__), quast_package,
'version.py')
with open('VERSION.txt') as f:
v = f.read().strip().split('\n')[0]
try:
compile_bwa(logger, only_clean=True)
compile_bedtools(logger, only_clean=True)
for fpath in [fn for fn in glob(join(quast_package, '*.pyc'))]: os.remove(fpath)
for fpath in [fn for fn in glob(join(quast_package, 'html_saver', '*.pyc'))]: os.remove(fpath)
for fpath in [fn for fn in glob(join(quast_package, 'site_packages', '*', '*.pyc'))]: os.remove(fpath)
if cmd_in(['clean']):
if isdir('build'):
shutil.rmtree('build')
if isdir('dist'):
shutil.rmtree('dist')
if isdir(name + '.egg-info'):
shutil.rmtree(name + '.egg-info')
download_gridss(logger, only_clean=True)
download_blast_binaries(logger, only_clean=True)
download_blastdb(logger, only_clean=True)
if qconfig.platform_name != 'macosx':
download_augustus(logger, only_clean=True)
download_all_db(logger, only_clean=True)
logger.info('Done.')
sys.exit()
if cmd_in(['test']):
ret_code = os.system('quast.py --test')
sys.exit(ret_code)
def write_version_py():
version_py = os.path.join(os.path.dirname(__file__), quast_package, 'version.py')