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"))
