#!/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 . # ########################################################################## 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"])