def run(self): from compile_externals import compile_all if not os.path.exists(self.build_tools_dir): os.mkdir(self.build_tools_dir) # Try to compile everything compile_all() # Copy everything that has been compiled for bin in MOTIF_BINS.values(): if os.path.exists(bin): shutil.copy(bin, self.build_tools_dir) # Copy seqlogo if os.path.exists("src/weblogo"): dlog.info("building seqlogo") patterns = [ "src/weblogo/logo.*", "src/weblogo/template.*", "src/weblogo/seqlogo" ] for p in patterns: for file in glob(p): shutil.copy(file, self.build_tools_dir) # Copy trawler if os.path.exists("src/trawler_standalone-1.2"): dlog.info("building trawler") if os.path.exists(os.path.join(self.build_tools_dir, "trawler")): shutil.rmtree(os.path.join(self.build_tools_dir, "trawler")) shutil.copytree("src/trawler_standalone-1.2", os.path.join(self.build_tools_dir, "trawler")) # Copy MotifSampler & Improbizer (ameme) if self.machine == "x86_64": if os.path.exists("src/MotifSampler"): dlog.info("copying MotifSampler 64bit") shutil.copy("src/MotifSampler/MotifSampler_x86_64", os.path.join(self.build_tools_dir, "MotifSampler")) shutil.copy( "src/MotifSampler/CreateBackgroundModel_x86_64", os.path.join(self.build_tools_dir, "CreateBackgroundModel")) if os.path.exists("src/Improbizer"): dlog.info("copying Improbizer (ameme) 64bit") shutil.copy("src/Improbizer/ameme_x86_64", os.path.join(self.build_tools_dir, "ameme")) else: if os.path.exists("src/MotifSampler"): dlog.info("copying MotifSampler 32bit") shutil.copy("src/MotifSampler/MotifSampler_i386", os.path.join(self.build_tools_dir, "MotifSampler")) shutil.copy( "src/MotifSampler/CreateBackgroundModel_i386", os.path.join(self.build_tools_dir, "CreateBackgroundModel")) if os.path.exists("src/Improbizer"): dlog.info("copying Improbizer (ameme) 32bit") shutil.copy("src/Improbizer/ameme_i386", os.path.join(self.build_tools_dir, "ameme"))
def run(self): from compile_externals import compile_all if not os.path.exists(self.build_tools_dir): os.mkdir(self.build_tools_dir) # Try to compile everything compile_all() # Copy everything that has been compiled for bin in MOTIF_BINS.values(): if os.path.exists(bin): shutil.copy(bin, self.build_tools_dir) # Copy seqlogo if os.path.exists("src/weblogo"): dlog.info("building seqlogo") patterns = ["src/weblogo/logo.*", "src/weblogo/template.*", "src/weblogo/seqlogo"] for p in patterns: for file in glob(p): shutil.copy(file, self.build_tools_dir) # Copy trawler if os.path.exists("src/trawler_standalone-1.2"): dlog.info("building trawler") if os.path.exists(os.path.join(self.build_tools_dir, "trawler")): shutil.rmtree(os.path.join(self.build_tools_dir, "trawler")) shutil.copytree("src/trawler_standalone-1.2", os.path.join(self.build_tools_dir, "trawler")) # Copy MotifSampler & Improbizer (ameme) if self.machine == "x86_64": if os.path.exists("src/MotifSampler"): dlog.info("copying MotifSampler 64bit") shutil.copy("src/MotifSampler/MotifSampler_x86_64", os.path.join(self.build_tools_dir, "MotifSampler")) shutil.copy("src/MotifSampler/CreateBackgroundModel_x86_64", os.path.join(self.build_tools_dir, "CreateBackgroundModel")) if os.path.exists("src/Improbizer"): dlog.info("copying Improbizer (ameme) 64bit") shutil.copy("src/Improbizer/ameme_x86_64", os.path.join(self.build_tools_dir, "ameme")) else: if os.path.exists("src/MotifSampler"): dlog.info("copying MotifSampler 32bit") shutil.copy("src/MotifSampler/MotifSampler_i386", os.path.join(self.build_tools_dir, "MotifSampler")) shutil.copy("src/MotifSampler/CreateBackgroundModel_i386", os.path.join(self.build_tools_dir, "CreateBackgroundModel")) if os.path.exists("src/Improbizer"): dlog.info("copying Improbizer (ameme) 32bit") shutil.copy("src/Improbizer/ameme_i386", os.path.join(self.build_tools_dir, "ameme"))
def run(self): if not self.dry_run: src_dir = os.path.join(self.build_base, "src") target_dir = os.path.join(self.build_lib, 'gimmemotifs/included_tools') #package_data={'gimmemotifs.data':['data/cfg/*']}, self.copy_tree("src/", src_dir) # mkpath is a distutils helper to create directories self.mkpath(target_dir) compile_all(src_dir=src_dir) for exes in MOTIF_BINS.values(): for exe in exes: if os.path.exists(exe): self.copy_file(exe, target_dir) exe = os.path.join(self.build_base, exe) if os.path.exists(exe): self.copy_file(exe, target_dir) self.copy_tree( os.path.join(src_dir, "ChIPMunk"), os.path.join(target_dir, "ChIPMunk")) self.copy_tree( os.path.join(src_dir,"HMS"), os.path.join(target_dir, "HMS")) self.copy_file( os.path.join(src_dir,"MotifSampler/MotifSampler_x86_64"), os.path.join(target_dir, "MotifSampler")) self.copy_file( os.path.join(src_dir,"MotifSampler/CreateBackgroundModel_x86_64"), os.path.join(target_dir, "CreateBackgroundModel")) self.copy_file( os.path.join(src_dir,"Improbizer/ameme_x86_64"), os.path.join(target_dir, "ameme")) if os.path.exists("src/weblogo"): self.copy_tree("src/weblogo", os.path.join(target_dir, "weblogo")) my_build_py.run(self)
def run(self): from compile_externals import compile_all prefix = distutils.sysconfig.get_config_var("prefix") if not os.path.exists(self.build_tools_dir): os.mkdir(self.build_tools_dir) # Try to compile everything compile_all(os.path.join(prefix, "share/gimmemotifs")) # Copy everything that has been compiled for bin in MOTIF_BINS.values(): if os.path.exists(bin): shutil.copy(bin, self.build_tools_dir) # Copy seqlogo if os.path.exists("src/weblogo"): dlog.info("building seqlogo") patterns = [ "src/weblogo/logo.*", "src/weblogo/template.*", "src/weblogo/seqlogo" ] for p in patterns: for file in glob(p): shutil.copy(file, self.build_tools_dir) # Copy posmo deps if os.path.exists("src/posmo"): shutil.copy("src/posmo/clusterwd", self.build_tools_dir) # Copy ChIPMunk if os.path.exists("src/ChIPMunk"): if os.path.exists(os.path.join(self.build_tools_dir, "ChIPMunk")): shutil.rmtree(os.path.join(self.build_tools_dir, "ChIPMunk")) shutil.copytree("src/ChIPMunk", os.path.join(self.build_tools_dir, "ChIPMunk")) # Copy HMS if os.path.exists("src/HMS"): if os.path.exists(os.path.join(self.build_tools_dir, "HMS")): shutil.rmtree(os.path.join(self.build_tools_dir, "HMS")) shutil.copytree("src/HMS", os.path.join(self.build_tools_dir, "HMS")) if self.machine == "x86_64": post_fix = "_x86_64" else: post_fix = "_i386" # Copy MotifSampler if not conda_build and os.path.exists("src/MotifSampler"): dlog.info("copying MotifSampler") shutil.copy("src/MotifSampler/MotifSampler{}".format(post_fix), os.path.join(self.build_tools_dir, "MotifSampler")) shutil.copy( "src/MotifSampler/CreateBackgroundModel{}".format(post_fix), os.path.join(self.build_tools_dir, "CreateBackgroundModel")) # Copy Improbizer (ameme) if os.path.exists("src/Improbizer"): dlog.info("copying Improbizer (ameme)") shutil.copy("src/Improbizer/ameme{}".format(post_fix), os.path.join(self.build_tools_dir, "ameme"))
def run(self): from compile_externals import compile_all prefix = distutils.sysconfig.get_config_var("prefix") if not os.path.exists(self.build_tools_dir): os.mkdir(self.build_tools_dir) # Try to compile everything compile_all(os.path.join(prefix, "share/gimmemotifs")) # Copy everything that has been compiled for bin in MOTIF_BINS.values(): if os.path.exists(bin): shutil.copy(bin, self.build_tools_dir) # Copy seqlogo if os.path.exists("src/weblogo"): dlog.info("building seqlogo") patterns = ["src/weblogo/logo.*", "src/weblogo/template.*", "src/weblogo/seqlogo"] for p in patterns: for file in glob(p): shutil.copy(file, self.build_tools_dir) # Copy posmo deps if os.path.exists("src/posmo"): shutil.copy("src/posmo/clusterwd", self.build_tools_dir) # Copy ChIPMunk if os.path.exists("src/ChIPMunk"): if os.path.exists(os.path.join(self.build_tools_dir, "ChIPMunk")): shutil.rmtree(os.path.join(self.build_tools_dir, "ChIPMunk")) shutil.copytree("src/ChIPMunk", os.path.join(self.build_tools_dir, "ChIPMunk")) # Copy HMS if os.path.exists("src/HMS"): if os.path.exists(os.path.join(self.build_tools_dir, "HMS")): shutil.rmtree(os.path.join(self.build_tools_dir, "HMS")) shutil.copytree("src/HMS", os.path.join(self.build_tools_dir, "HMS")) # Copy trawler if os.path.exists("src/trawler_standalone-1.2"): dlog.info("building trawler") if os.path.exists(os.path.join(self.build_tools_dir, "trawler")): shutil.rmtree(os.path.join(self.build_tools_dir, "trawler")) shutil.copytree("src/trawler_standalone-1.2", os.path.join(self.build_tools_dir, "trawler")) if self.machine == "x86_64": post_fix = "_x86_64" else: post_fix = "_i386" # Copy MotifSampler if not conda_build and os.path.exists("src/MotifSampler"): dlog.info("copying MotifSampler") shutil.copy( "src/MotifSampler/MotifSampler{}".format(post_fix), os.path.join( self.build_tools_dir, "MotifSampler") ) shutil.copy( "src/MotifSampler/CreateBackgroundModel{}".format(post_fix), os.path.join( self.build_tools_dir, "CreateBackgroundModel") ) # Copy Improbizer (ameme) if os.path.exists("src/Improbizer"): dlog.info("copying Improbizer (ameme)") shutil.copy("src/Improbizer/ameme{}".format(post_fix), os.path.join(self.build_tools_dir, "ameme"))