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ImageTest.java
setup.py 10.80 KiB
#!/usr/bin/env python
############################################################################
# Copyright (c) 2015-2017 Saint Petersburg State University
# Copyright (c) 2011-2015 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
from __future__ import with_statement
import os
import sys
from glob import glob
from os.path import join, isfile, abspath, dirname, isdir
import shutil
from quast_libs import qconfig
qconfig.check_python_version()
from quast_libs import qutils
from quast_libs.log import get_logger
logger = get_logger(qconfig.LOGGER_DEFAULT_NAME)
logger.set_up_console_handler(debug=True)
try:
from setuptools import setup, find_packages
except:
logger.error('setuptools is not installed or outdated!\n\n'
'You can install or update setuptools using\n'
'pip install --upgrade setuptools (if you have pip)\n'
'or\n'
'sudo apt-get install python-setuptools (on Ubuntu)\n'
'\n'
'You may also use old-style installation scripts: ./install.sh or ./install_full.sh',
exit_with_code=1)
from quast_libs.search_references_meta import download_all_blast_binaries, download_blastdb
from quast_libs.glimmer import compile_glimmer
from quast_libs.gage import compile_gage
from quast_libs.ca_utils.misc import compile_aligner, compile_gnuplot
from quast_libs.ra_utils.misc import compile_reads_analyzer_tools, download_manta, compile_bwa, compile_bedtools
name = 'quast'
quast_package = qconfig.PACKAGE_NAME
args = sys.argv[1:]
def cmd_in(cmds):
return any(c in args for c in cmds)
if abspath(dirname(__file__)) != abspath(os.getcwd()):
logger.error('Please change to ' + dirname(__file__) + ' before running setup.py')
sys.exit()
if cmd_in(['clean', 'sdist']):
logger.info('Cleaning up binary files...')
compile_aligner(logger, only_clean=True)
compile_gnuplot(logger, only_clean=True)
compile_glimmer(logger, only_clean=True)
compile_gage(only_clean=True)
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=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:
import subprocess
git_revision = subprocess.check_output(['git', 'rev-parse', '--short', 'HEAD'],
stderr=open(os.devnull, 'w')).rstrip()
except:
git_revision = ''
pass
if not isinstance(git_revision, str):
git_revision = git_revision.decode('utf-8')
with open(version_py, 'w') as f:
f.write((
'# Do not edit this file, pipeline versioning is governed by git tags\n'+
'__version__ = \'' + v + '\'\n' +
'__git_revision__ = \'%s\'' % git_revision))
return v
version = write_version_py()
if cmd_in(['tag']):
cmdl = 'git tag -a %s -m "Version %s" && git push --tags' % (version, version)
os.system(cmdl)
sys.exit()
if cmd_in(['publish']):
cmdl = 'python setup.py sdist && python setup.py sdist upload'
os.system(cmdl)
sys.exit()
def find_package_files(dirpath, package=quast_package):
paths = []
for (path, dirs, fnames) in os.walk(join(package, dirpath)):
for fname in fnames:
paths.append(qutils.relpath(join(path, fname), package))
return paths
install_full = False
if cmd_in(['install_full']):
install_full = True
args2 = []
for a_ in args:
if a_ == 'install_full':
args2.append('install')
else:
args2.append(a_)
args = args2
modules_failed_to_install = []
if cmd_in(['install', 'develop', 'build', 'build_ext']):
try:
import matplotlib
except ImportError:
try:
pip.main(['install', 'matplotlib'])
except:
logger.warning('Cannot install matplotlib. Static plots will not be drawn (however, HTML will be)')
logger.info('* Compiling aligner *')
if not compile_aligner(logger):
modules_failed_to_install.append('Contigs aligners for reference-based evaluation (affects -R and many other options)')
logger.info('* Compiling gnuplot *')
if not compile_gnuplot(logger):
logger.warning('Cannot compile gnuplot. MUMmer plots will not be drawn')
logger.info('* Compiling Glimmer *')
if not compile_glimmer(logger):
modules_failed_to_install.append('Glimmer gene-finding tool (affects --glimmer option)')
logger.info('* Compiling read analysis tools *')
if not compile_reads_analyzer_tools(logger):
modules_failed_to_install.append('Read analysis tools (affects -1/--reads1 and -2/--reads2 options)')
if install_full:
logger.info('* Downloading Manta *')
if not download_manta(logger):
modules_failed_to_install.append('Manta (affects -1/--reads1 and -2/--reads2 options)')
logger.info('* Downloading SILVA 16S rRNA gene database and BLAST *')
if not download_all_blast_binaries(logger) or not download_blastdb(logger):
modules_failed_to_install.append('SILVA 16S rRNA gene database and BLAST (affects metaquast.py in without references mode)')
logger.info('* Compiling GAGE *')
if not compile_gage():
modules_failed_to_install.append('GAGE scripts (affects --gage option [will be deprecated soon])')
logger.info('')
if qconfig.platform_name == 'macosx':
sambamba_files = [join('sambamba', 'sambamba_osx')]
else:
sambamba_files = [join('sambamba', 'sambamba_linux')]
nucmer_files = find_package_files('MUMmer')
bwa_files = [
join('bwa', fp) for fp in os.listdir(join(quast_package, 'bwa'))
if isfile(join(quast_package, 'bwa', fp)) and fp.startswith('bwa')]
full_install_tools = (
find_package_files('manta') +
find_package_files('blast') +
sambamba_files
)
setup(
name=name,
version=version,
author='Alexey Gurevich, Vladislav Saveliev, Alla Mikheenko, and others',
author_email='quast.support@bioinf.spbau.ru',
description='Genome assembly evaluation tool',
long_description='''QUAST evaluates genome assemblies.
It works both with and without reference genomes.
The tool accepts multiple assemblies, thus is suitable for comparison.''',
keywords=['bioinformatics', 'genome assembly', 'metagenome assembly', 'visualization'],
url='quast.sf.net',
platforms=['Linux', 'OS X'],
license='GPLv2',
packages=find_packages(),
package_data={
quast_package:
find_package_files('html_saver') +
nucmer_files +
find_package_files('genemark/' + qconfig.platform_name) +
find_package_files('genemark-es/' + qconfig.platform_name) +
find_package_files('genemark-es/lib') +
find_package_files('glimmer') +
find_package_files('gage') +
bwa_files +
['bedtools/bin/*'] +
(full_install_tools if install_full else [])
},
include_package_data=True,
zip_safe=False,
scripts=['quast.py', 'metaquast.py', 'icarus.py'],
data_files=[
('', [
'README.md',
'CHANGES.txt',
'VERSION.txt',
'LICENSE.txt',
'manual.html',
]),
('test_data', find_package_files('test_data', package='')),
],
install_requires=[
'joblib',
'simplejson',
],
classifiers=[
'Environment :: Console',
'Environment :: Web Environment',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: GNU General Public License v2 (GPLv2)',
'Natural Language :: English',
'Operating System :: MacOS :: MacOS X',
'Operating System :: POSIX',
'Operating System :: Unix',
'Programming Language :: Python',
'Programming Language :: JavaScript',
'Topic :: Scientific/Engineering',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Topic :: Scientific/Engineering :: Visualization',
],
script_args=args,
)
if cmd_in(['install']):
not_installed_message = ''
if modules_failed_to_install:
not_installed_message = 'WARNING: some modules were not installed properly and\n' \
'QUAST functionality will be restricted!\n' \
'The full list of malformed modules and affected options:\n'
not_installed_message += "\n".join(map(lambda x: " * " + x, modules_failed_to_install))
not_installed_message += "\n\n"
if not install_full:
logger.info('''
----------------------------------------------
QUAST version %s installation complete.
%sPlease run ./setup.py test to verify installation.
For help in running QUAST, please see the documentation available
at quast.sf.net/manual.html, or run quast.py --help
Usage:
$ quast.py test_data/contigs_1.fasta \\
test_data/contigs_2.fasta \\
-R test_data/reference.fasta.gz \\
-G test_data/genes.txt \\
-o quast_test_output
----------------------------------------------''' % (str(version), not_installed_message))
else:
logger.info('''
----------------------------------------------
QUAST version %s installation complete.
The full package is installed, with the features for reference
sequence detection in MetaQUAST, and structural variant detection
for misassembly events refinement.
%sPlease run ./setup.py test to verify installation.
For help in running QUAST, please see the documentation available
at quast.sf.net/manual.html, or run quast.py --help
Usage:
$ quast.py test_data/contigs_1.fasta \\
test_data/contigs_2.fasta \\
-R test_data/reference.fasta.gz \\
-G test_data/genes.txt \\
-1 test_data/reads1.fastq.gz -2 test_data/reads2.fastq.gz \\
-o quast_test_output
----------------------------------------------''' % (str(version), not_installed_message))