def run(self):
if cmd_exists("make") and cmd_exists('gcc') and cmd_exists('g++'):
os.system("cd mgescan/ltr/MER; make clean; make")
os.system("cd mgescan/nonltr/; make clean; make translate")
os.system("cd mgescan/nonltr/hmm;make clean; make")
else:
print ("[Warning] make|gcc|g++ does not exist. Compile code is skipped")
time.sleep(3)
if cmd_exists("mpicc"):
os.system("cd mgescan;mpicc mpi_mgescan.c -o mpi_mgescan")
else:
print ("[Warning] mpicc does not exist. Compile mpi code is"\
+ " skipped")
time.sleep(3)
if not os.environ.get('MGESCAN_HOME'):
print ("$MGESCAN_HOME is not defined where MGESCAN will be" + \
" installed.")
def_home = raw_input("Would you install MGESCAN at " + \
os.environ.get("HOME") + "/mgescan3 (Y/n)?")
if def_home.lower() == 'n':
print ("Run 'export MGESCAN_HOME=<your desired destination" + \
" path to install>' if you want to install somewhere"+\
" else\n")
sys.exit()
os.environ['MGESCAN_HOME'] = os.environ.get('HOME') + "/mgescan3"
if os.environ.get('MGESCAN_HOME') and not os.environ.get("MGESCAN_SRC"):
os.environ['MGESCAN_SRC'] = os.environ.get('MGESCAN_HOME') + "/src"
if not os.path.exists(os.environ.get("MGESCAN_SRC")):
os.makedirs(os.environ.get("MGESCAN_SRC"), 0755)
if os.environ.get("MGESCAN_SRC"):
os.system("cp -pr * $MGESCAN_SRC")
bdist_egg.run(self)
def run(self):
# run default setup procedure
bdist_egg.run(self)
import sys
# Check whether setup.py is run from inside a virtualenv and get the
# appropriate install location for exploitable.py.
if hasattr(sys, 'real_prefix'):
# Inside virtualenv:
# Use Python standard library location.
from distutils.sysconfig import get_python_lib
install_base_path = get_python_lib()
else:
# Not inside virtualenv, operating on a real Python environment:
# Use location for Python site-specific, platform-specific files.
from sysconfig import get_path
install_base_path = get_path('platlib')
path_to_exploitable = os.path.join(install_base_path,
os.path.basename(self.egg_output),
'exploitable',
'exploitable.py')
print('\x1b[0;32m**********************************************')
print(' Install complete! Source exploitable.py from')
print(' your .gdbinit to make it available in GDB:')
print('')
print(' \x1b[1;37mecho \"source %s\" >> ~/.gdbinit\x1b[0;32m' % path_to_exploitable)
print('**********************************************\x1b[0m')
def run(self):
# run default setup procedure
bdist_egg.run(self)
import sys
# Check whether setup.py is run from inside a virtualenv and get the
# appropriate install location for exploitable.py.
if hasattr(sys, 'real_prefix'):
# Inside virtualenv:
# Use Python standard library location.
from distutils.sysconfig import get_python_lib
install_base_path = get_python_lib()
else:
# Not inside virtualenv, operating on a real Python environment:
# Use location for Python site-specific, platform-specific files.
from sysconfig import get_path
install_base_path = get_path('platlib')
path_to_exploitable = os.path.join(install_base_path,
os.path.basename(self.egg_output),
'exploitable', 'exploitable.py')
print('\x1b[0;32m**********************************************')
print(' Install complete! Source exploitable.py from')
print(' your .gdbinit to make it available in GDB:')
print('')
print(' \x1b[1;37mecho \"source %s\" >> ~/.gdbinit\x1b[0;32m' %
path_to_exploitable)
print('**********************************************\x1b[0m')
def run(self):
print("generate web application")
if os.system('npm install') != 0:
raise Exception("Could not install npm packages")
if os.system('npm run build') != 0:
raise Exception("Could not build web application")
bdist_egg.run(self)
def run(self):
try:
prior = getattr(self.distribution, 'running_binary', False)
self.distribution.running_binary = True
self.run_command('build')
dBuildDistEgg.run(self)
finally: self.distribution.running_binary = prior
def run(self):
# Ensure that there is a basic library build for bdist_egg to pull from.
self.run_command("build")
_cleanup_symlinks(self)
# Run the default bdist_egg command
orig_bdist_egg.run(self)
def run(self):
try:
prior = getattr(self.distribution, 'running_binary', False)
self.distribution.running_binary = True
self.run_command('build')
dBuildDistEgg.run(self)
finally: self.distribution.running_binary = prior
def run(self):
# Ensure that there is a basic library build for bdist_egg to pull from.
self.run_command("build")
_cleanup_symlinks(self)
# Run the default bdist_egg command
orig_bdist_egg.run(self)
def run(self):
try:
self.run_command('build_sphinx')
if 'build_man' in cmdclass:
self.run_command('build_man')
except:
log.warn("Couldn't build documentation:\n%s" %
traceback.format_exception(*sys.exc_info()))
bdist_egg.run(self)
def run(self):
try:
self.run_command('build_sphinx')
if 'build_man' in cmdclass:
self.run_command('build_man')
except:
log.warn("Couldn't build documentation:\n%s" %
traceback.format_exception(*sys.exc_info()))
bdist_egg.run(self)
def run(self):
_bdist_egg.run(self)
with open(self.egg_output, 'rb') as f:
data = f.read()
with open(self.egg_output, 'wb') as f:
f.write('#!/usr/bin/env python\n'.encode() + data)
z = zipfile.ZipFile(self.egg_output, 'a')
z.writestr('__main__.py', 'from needy.__main__ import main\nimport sys\nsys.exit(main(sys.argv))')
z.close()
def run(self):
bdist_egg.run(self)
if not os.path.isdir(self.sentinel_dir):
print("\n".join([ # noqa
"************************************************************",
"The front end assets for Wagtail are missing.",
"To generate the assets, please refer to the documentation in",
"docs/contributing/css_guidelines.rst",
"************************************************************",
]))
def run(self):
bdist_egg.run(self)
if not os.path.isdir(self.sentinel_dir):
print("\n".join([
"************************************************************",
"The front end assets for Wagtail are missing.",
"To generate the assets, please refer to the documentation in",
"docs/contributing/css_guidelines.rst",
"************************************************************",
]))
def run(self):
_bdist_egg.run(self)
with open(self.egg_output, 'rb') as f:
data = f.read()
with open(self.egg_output, 'wb') as f:
f.write('#!/usr/bin/env python\n'.encode() + data)
z = zipfile.ZipFile(self.egg_output, 'a')
z.writestr(
'__main__.py',
'from needy.__main__ import main\nimport sys\nsys.exit(main(sys.argv))'
)
z.close()
def run(self):
self.create_init_files(self.test_dir)
# Re-run the package search now we've ensured there are package files
# extant
self.distribution.packages = [
'%s.%s.%s' % (CONFIG.test_egg_namespace, self.old_name, i)
for i in find_packages('tests')
]
# Bin the build directory, this stops artifacts from the real package
# getting in there
self.execute(shutil.rmtree, (self.build_lib, ),
"removing %s (and everything under it)" % self.build_lib)
# Re-run the egg-info step, setting the option to include test options
self.reinitialize_command('egg_info')
self.ei_cmd = self.get_finalized_command('egg_info')
self.ei_cmd.include_test_options = True
self.ei_cmd.tag_build = None
self.ei_cmd.egg_version = self.old_version
self.ei_cmd.run()
# Copy all the test files into the build directory and ensure they're
# real packages
for root, dirs, files in os.walk(self.test_dir):
if '.svn' in dirs:
dirs.remove('.svn')
if '__pycache__' in dirs:
dirs.remove('__pycache__')
for f in files:
f = os.path.join(root, f)
self.execute(self._copy_file, (f, self.get_file_dest(f)),
"copying %s -> %s" % (f, self.get_file_dest(f)))
self.create_ns_pkg_files(self.build_lib)
pytest_cfg = os.path.join(self.dest_dir, 'pytest.ini')
self.execute(self.create_pytest_config, (pytest_cfg, ),
"creating pytest config at %s" % pytest_cfg)
# Kick off a bdist_egg which will build the egg for us
_bdist_egg.run(self)
# Clean up the egg-info dir, pkg_resources finds it in source
# checkouts and thinks the package is installed somewhere
self.execute(shutil.rmtree, (self.egg_info, ),
"removing %s (and everything under it)" % self.egg_info)
def run(self):
self.create_init_files(self.test_dir)
# Re-run the package search now we've ensured there are package files
# extant in the distro
self.distribution.packages = ['%s.%s.%s' % (CONFIG.test_egg_namespace,
self.old_name, i)
for i in find_packages('tests')]
# Bin the build directory, this stops artifacts from the real package
# getting in there
self.execute(self.build_lib.rmtree, (self.build_lib,),
"removing %s (and everything under it)" % self.build_lib)
# Re-run the egg-info step, setting the option to include test options
self.reinitialize_command('egg_info')
self.ei_cmd = self.get_finalized_command('egg_info')
self.ei_cmd.include_test_options = True
self.ei_cmd.tag_build = None
self.ei_cmd.egg_version = self.old_version
self.ei_cmd.run()
# Copy all the test files into the build directory and ensure they're
# real packages
for filename in self.test_dir.walk():
if (not filename.isfile()
or '.svn' in filename
or '__pycache__' in filename):
continue
self.execute(self._copy_file, (filename,
self.get_file_dest(filename)),
"copying {} -> {}"
.format(filename, self.get_file_dest(filename)))
self.create_ns_pkg_files(self.build_lib)
pytest_cfg = self.dest_dir / 'pytest.ini'
self.execute(self.create_pytest_config, (pytest_cfg,),
"creating pytest config at %s" % pytest_cfg)
# Kick off a bdist_egg which will build the egg for us
_bdist_egg.run(self)
# Clean up the egg-info dir, pkg_resources finds it in source checkouts
# and thinks the package is installed somewhere
self.execute(self.egg_info.rmtree, (self.egg_info,),
"removing %s (and everything under it)" % self.egg_info)
def run(self):
self.create_init_files(self.test_dir)
# Re-run the package search now we've ensured there are package files
# extant
self.distribution.packages = [
"%s.%s.%s" % (CONFIG.test_egg_namespace, self.old_name, i) for i in find_packages("tests")
]
# Bin the build directory, this stops artifacts from the real package
# getting in there
self.execute(shutil.rmtree, (self.build_lib,), "removing %s (and everything under it)" % self.build_lib)
# Re-run the egg-info step, setting the option to include test options
self.reinitialize_command("egg_info")
self.ei_cmd = self.get_finalized_command("egg_info")
self.ei_cmd.include_test_options = True
self.ei_cmd.tag_build = None
self.ei_cmd.egg_version = self.old_version
self.ei_cmd.run()
# Copy all the test files into the build directory and ensure they're
# real packages
for root, dirs, files in os.walk(self.test_dir):
if ".svn" in dirs:
dirs.remove(".svn")
if "__pycache__" in dirs:
dirs.remove("__pycache__")
for f in files:
f = os.path.join(root, f)
self.execute(
self._copy_file, (f, self.get_file_dest(f)), "copying %s -> %s" % (f, self.get_file_dest(f))
)
self.create_ns_pkg_files(self.build_lib)
pytest_cfg = os.path.join(self.dest_dir, "pytest.ini")
self.execute(self.create_pytest_config, (pytest_cfg,), "creating pytest config at %s" % pytest_cfg)
# Kick off a bdist_egg which will build the egg for us
_bdist_egg.run(self)
# Clean up the egg-info dir, pkg_resources finds it in source
# checkouts and thinks the package is installed somewhere
self.execute(shutil.rmtree, (self.egg_info,), "removing %s (and everything under it)" % self.egg_info)
def run(self):
old_bdist_egg.run(self)
spec_depend = textwrap.dedent("""\
metadata_version = '1.1'
name = 'enstaller'
version = '{0}'
build = 1
arch = None
platform = None
osdist = None
python = None
packages = []
""".format(__version__))
self._write_spec_depend(spec_depend)
with open(BOOTSTRAP_SCRIPT, "rt") as fp:
self._write_bootstrap_code(fp.read())
def run(self):
# Ensure that there is a basic library build for bdist_egg to pull from.
self.run_command("build")
# Clean out any libwx* symlinks in the build_lib folder, as they will
# turn into copies in the egg since zip files can't handle symlinks.
# The links are not really needed since the extensions link to
# specific soname, and they could bloat the egg too much if they were
# left in.
#
# TODO: can eggs have post-install scripts that would allow us to
# restore the links?
#
build_lib = self.get_finalized_command('build').build_lib
build_lib = opj(build_lib, 'wx')
for libname in glob.glob(opj(build_lib, 'libwx*')):
if os.path.islink(libname):
if isDarwin:
# On Mac the name used by the extension module is the real
# file, so we can just get rid of all the links.
os.unlink(libname)
elif canGetSOName():
# On linux the soname used in the extension modules may
# be (probably is) one of the symlinks, so we have to be
# more tricky here. If the named file is a link and it is
# the soname, then remove the link and rename the
# linked-to file to this name.
soname = getSOName(libname)
if soname == os.path.basename(libname):
realfile = os.path.join(build_lib, os.readlink(libname))
os.unlink(libname)
os.rename(realfile, libname)
else:
os.unlink(libname)
else:
# Otherwise just leave the symlink there since we don't
# know what to do with it.
pass
# Run the default bdist_egg command
orig_bdist_egg.run(self)
def run(self):
self.run_command("build")
_bdist_egg.run(self)
def run(self):
self.run_command("build")
return _bdist_egg.run(self)
def run(self):
call(["pip install -r requirements.txt --no-clean"], shell=True)
_bdist_egg.run(self)
def run(self):
self.call_command('build_clib')
bdist_egg.run(self)
def run(self):
# This will not run when installing from pip, thus
# avoiding a few dependencies.
if not os.path.exists(THEME_DIST_DIR):
self.run_command('build_default_theme')
return bdist_egg.run(self)
def run(self):
compile_AHK()
bdist_egg.run(self)
clean_egg_info()
def run(self):
build_js()
bdist_egg.run(self)
def run(self):
"""Call build_sphinx then proceed as normal."""
self.run_command('build_sphinx')
bdist_egg.run(self)
def run(self):
_bdist_egg.run(self)
post_install(self, False)
def run(self):
self.run_command('build_ext')
bdist_egg.run(self)
def run(self):
self.run_command('build')
_bdist_egg.run(self)
def run(self):
bdist_egg.run(self)
if self.install_lua_libs:
self.run_command("install_lua_libs")
def run(self):
'''
Checking Prerequisites
'''
hmmer_exists = cmd_exists("hmmsearch")
emboss_exists = cmd_exists("transeq")
trf_exists = cmd_exists("trf")
blast_exists = cmd_exists("blastn")
if not (hmmer_exists and emboss_exists and trf_exists and blast_exists):
print ("[Error] Prerequisite software(s):")
if not hmmer_exists:
print ("\t- HMMER")
if not emboss_exists:
print ("\t- EMBOSS")
if not trf_exists:
print ("\t- Tandem Repeats Finder")
if not blast_exists:
print ("\t- NCBI-BLAST+")
print ("\tare not installed!")
print ("Please install the above software and re-run this setup.")
print ("Exiting without installation!")
sys.exit()
'''
Checking Install Path
'''
install_path = ""
if not os.environ.get('MGESCAN_HOME'):
print ("$MGESCAN_HOME is not defined where MGESCAN will be" + \
" installed.")
def_home = raw_input("Would you like to install MGEScan at " + \
os.environ.get("HOME") + "/mgescan4 (Y/n)?")
if def_home.lower() == 'n':
print ("Run 'export MGESCAN_HOME=<your desired destination" + \
" path to install>' if you want to install somewhere"+\
" else\n")
sys.exit()
install_path = os.environ.get('HOME') + "/mgescan4"
else:
print ("Installing MGEScan in "+os.environ.get('MGESCAN_HOME')+" (MGESCAN_HOME)")
install_path = os.environ.get('MGESCAN_HOME')
if not os.path.exists(install_path):
os.makedirs(install_path, 0755)
else:
print ("It looks like a previous installation of MGEScan already exists in "+install_path)
print ("Please remove the previous installation and re-run this setup.")
print ("Exiting without installation!")
sys.exit()
'''
Installing
'''
if cmd_exists("make") and cmd_exists('gcc') and cmd_exists('g++'):
os.system("cd mgescan/ltr/MER; make clean; make")
os.system("cd mgescan/nonltr/; make clean; make translate")
os.system("cd mgescan/nonltr/hmm;make clean; make")
else:
print ("[Warning] make|gcc|g++ does not exist. Compile code is skipped")
time.sleep(3)
if cmd_exists("mpicc"):
os.system("cd mgescan;mpicc mpi_mgescan.c -o mpi_mgescan")
else:
print ("[Warning] mpicc does not exist. Compile mpi code is"\
+ " skipped")
time.sleep(3)
os.system("cp -pr * "+install_path)
if not os.environ.get('GALAXY_HOME'):
print ("[Warning] $GALAXY_HOME is not defined. Copying MGEScan Galaxy files is skipped.")
time.sleep(3)
else:
os.system("cp -pr galaxy-modified/* $GALAXY_HOME")
bdist_egg.run(self)
def run(self):
if not self.dry_run:
self.run_command('prebuild')
bdist_egg.run(self)
def run(self):
suffix = self.get_datetime_suffix()
self.distribution.metadata.version += "_%s" % suffix
bdist_egg.run(self)
def run(self):
# Run build_ext first so that SWIG generated files are included
self.run_command("build_ext")
return bdist_egg.run(self)
def run(self):
self.call_command('build_clib')
bdist_egg.run(self)
def run(self):
self.run_command('build')
return bdist_egg.run(self)
def run(self):
bdist_egg.run(self)
enable_visual_interface()
def run(self):
bdist_egg.run(self)
def run(self):
self.run_command('genschema')
bdist_egg.run(self)
def run(self):
build_openzwave = self.distribution.get_command_obj('build_openzwave')
build_openzwave.develop = True
self.run_command('build_openzwave')
_bdist_egg.run(self)
def run(self):
self.distribution.ext_modules = swig_modules
self.run_command('build_ext')
bdist_egg.run(self)
def run(self):
self.run_command('CustomCommands')
_bdist_egg.run(self)
def run(self):
"""Call build_man then proceed as normal."""
self.run_command('build_man')
bdist_egg.run(self)
def run(self):
self.run_command('compilemessages')
_bdist_egg.run(self)
def run(self):
self.run_command('DownloadTemplates')
_bdist_egg.run(self)
def run(self):
_bdist_egg.run(self)
self.execute(post_install, (self, False), msg="Running post install tasks")
def run(self):
self.run_command('build')
_bdist_egg.run(self)
def run(self):
self.run_command('build_ext')
return _bdist_egg.run(self)
def run(self):
self.run_command('download_default_template')
return bdist_egg.run(self)
def run(self):
create_ecodes()
bdist_egg.run(self)
def run(self):
bdist_egg.run(self)
self.run_command('gentab')
def run(self):
self.run_command('build')
return bdist_egg.run(self)
def run(self):
# Allow installing as a dependency via pip.
self.run_command("build_ext")
bdist_egg.run(self)
def run(self):
self.run_command('build_bootloader')
bdist_egg.run(self)
