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#!/usr/bin/env python
# ##########################################################################
# Copyright 2012 Siavash Mirarab, Nam Nguyen, and Tandy Warnow.
# This file is part of SEPP.
#
# SEPP is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# SEPP is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with SEPP. If not, see <http://www.gnu.org/licenses/>.
# ##########################################################################
import os
import platform
import sys
# from distutils.core import setup
from distribute_setup import use_setuptools
import shutil
from setuptools import find_packages
from distutils.core import setup, Command
from distutils.spawn import find_executable
import tipp
use_setuptools(version="0.6.24")
version = "1.1.0"
def get_tools_dir(where):
path = os.path.join(os.getcwd(), "tools", where)
# if not os.path.exists(path):
# raise OSError("TIPP does not bundle tippJsonMerger for '%s' at this time!" )
return path
def get_tool_name(tool, bits):
if platform.system() == "Darwin" or True: # Never add anything to tool name under Debian
return tool
is_64bits = sys.maxsize > 2**32
return "%s-%s" % (tool, "64" if is_64bits else "32")
class ConfigSepp(Command):
"""setuptools Command"""
description = "Configures Sepp for the current user"
user_options = [(
'contained', 'c',
("Whether SEPP should be installed in a self-contained "
"manner or on user's home"))]
def initopts(self):
self.contained = True
self.configfile = None
self.basepath = None
def initpath(self, name):
if self.contained:
self.configfile = os.path.expanduser(
os.path.abspath(os.path.join(".tipp", name)))
self.basepath = os.path.dirname(self.configfile)
else:
self.configfile = os.path.expanduser("~/.tipp/%s" % name)
self.basepath = os.path.expanduser("~/.tipp")
with open('home.path', 'w') as fo:
fo.write(self.basepath)
fo.close()
def get_tools_dest(self):
return os.path.join(self.basepath, "bundled-v%s" % version)
def copy_tool_to_lib(self, tool, where, bits=True):
# The jar just build is in a subdirectory, while we want to use
# Debian-provided binaries.
if get_tool_name(tool, bits).find(".jar") != -1:
shutil.copy2(
os.path.join(get_tools_dir(where), get_tool_name(tool, bits)),
os.path.join(self.get_tools_dest(), tool))
else:
shutil.copy2(
os.path.join("/usr/bin", get_tool_name(tool, bits)),
os.path.join(self.get_tools_dest(), tool))
def initialize_options(self):
"""init options"""
self.initopts()
def finalize_options(self):
"""finalize options"""
self.initpath("main.config")
print("\nCreating main sepp config file at %s and tools at %s" % (
self.configfile, self.basepath))
def run(self):
def get_tool_name(tool, bits):
# MAC doesn't have 32/64
if platform.system() == "Darwin" or not bits:
return tool
is_64bits = sys.maxsize > 2**32
return "%s-%s" % (tool, "64" if is_64bits else "32")
# Create the default config file
if not os.path.exists(self.basepath):
os.mkdir(self.basepath)
if not os.path.exists(self.get_tools_dest()):
os.mkdir(self.get_tools_dest())
c = open("default.main.config")
d = open(self.configfile, "w")
for l1 in c:
l1 = l1.replace("~", self.get_tools_dest())
d.write(l1)
d.close()
# Copy tools to a bundled directory inside .tipp
self.copy_tool_to_lib("guppy")
self.copy_tool_to_lib("pplacer")
self.copy_tool_to_lib("hmmalign")
self.copy_tool_to_lib("hmmsearch")
self.copy_tool_to_lib("hmmbuild")
# TODO: should we compile and build merge.jar?
self.copy_tool_to_lib("seppJsonMerger.jar", where="merge", bits=False)
class ConfigTIPP(ConfigSepp):
"""setuptools Command"""
description = "Configures TIPP for the current user"
user_options = [('contained', 'c',
("Whether TIPP should be installed in a self-contained "
"manner or on user's home"))]
def initialize_options(self):
"""init options"""
self.initopts()
def finalize_options(self):
"""finalize options"""
self.initpath("tipp.config")
print("\nCreating main TIPP config file at %s and tools at %s" % (
self.configfile, self.basepath))
def run(self):
## We are going to read sepp config file and write it here
sepp_config_path = "/etc/sepp/sepp.config"
# Create the default config file
if not os.path.exists(self.basepath):
os.mkdir(self.basepath)
if not os.path.exists(self.get_tools_dest()):
os.mkdir(self.get_tools_dest())
c = open(sepp_config_path)
d = open(self.configfile, "w")
for l3 in c:
#This is not needed as we are reading sepp config and not default config distributed with
# l3 = l3.replace("~", self.get_tools_dest())
if (l3.find('seppJsonMerger.jar') != -1):
l3 = 'path=/usr/share/tipp/tippJsonMerger.jar\n'
d.write(l3)
if not os.getenv('SATE') is None:
d.write('\n[sate]\npath=%s' % os.getenv('SATE'))
if os.getenv('BLAST') is None and not find_executable("blastn"):
print("\nWarning! BLAST variable is not defined. If you plan to "
"run TIPP for abundance profiling,"
" then have BLAST pointed to blastn executable. "
"You can also change your config to point to"
" blastn by including the following line in your"
" config:\n[blast]\npath=/location/of/blast_directory/"
"blastn\n")
d.write('\n[blast]\npath=None\n')
else:
blastn_path = find_executable("blastn") if os.getenv('BLAST') \
is None else os.getenv('BLAST')
d.write('\n[blast]\npath=%s\n' % blastn_path)
if os.getenv('REFERENCE') is None:
print("\nWarning! REFERENCE variable is not defined. "
"If you plan to run TIPP for abundance profiling, then have "
"REFERENCE pointed to Reference directory. You can also "
"change your config to point to the Reference directory by "
"including the following line in your config:\n[reference]"
"\npath=/location/of/reference_directory/\n")
d.write('\n[reference]\npath=%s\n' % os.getenv('REFERENCE'))
d.write('\n[tipp]\npushdown = true\n')
d.close()
# Copy tools to a bundled directory inside .tipp
self.copy_tool_to_lib("tippJsonMerger.jar", where="merge", bits=False)
setup(name="tipp",
version=version,
description="SATe enabled phylogenetic placement.",
packages=find_packages(),
url="https://github.com/smirarab/sepp",
author="Siavash Mirarab and Nam Nguyen",
author_email="smirarab@gmail.com, namphuon@cs.utah.edu",
license="General Public License (GPL)",
install_requires=["dendropy >= 4.0.0", "sepp"],
provides=["tipp"],
scripts=["run_abundance.py","run_tipp.py","run_tipp_tool.py"],
cmdclass={"tipp": ConfigTIPP},
data_files=[('', ['home.path'])],
classifiers=["Environment :: Console",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
("License :: OSI Approved :: GNU General Public "
"License (GPL)"),
"Natural Language :: English",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Topic :: Scientific/Engineering :: Bio-Informatics"])
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