import os
import sys
import glob
from distutils.core import setup
from distutils.sysconfig import get_config_vars
from setuptools import setup, Command
from setuptools.command.install import install as _install
# from setuptools.command.build_py import build_py as _build_py
from setuptools.command.install_scripts import install_scripts as _install_scripts
from setuptools.command.install_lib import install_lib as _install_lib
from distutils.command.clean import clean as _clean
from site import USER_BASE
from site import USER_SITE
import subprocess
import shutil
pwd = os.path.abspath(os.path.dirname(__file__))
exec(open(os.path.join(pwd,'gemBS','version.py')).read())
def compile_gemBS_tools(options, enable_cuda, disable_cuda):
make_com = 'make ' + ' '.join(options)
if disable_cuda:
make_com = "GEM3_CONFIG=\'--disable-cuda\' " + make_com
elif enable_cuda:
make_com = "GEM3_CONFIG=\'--enable-cuda\' " + make_com
process = subprocess.Popen(make_com, shell=True, cwd='tools')
if process.wait() != 0:
print ("""
Error while compiling gemBS. That is very unfortunate.
A possible reason might be a missing dependency. Please take a look at the lines
before this one. You need the following programs and libraries installed to compile
the gemBS.
Programms needed:
* make
* gcc
Libraris needed:
* python-dev (the python headers and include files)
* libbz2-dev (for bz compression support)
On a Debian/Ubuntu system you should be able to get all needed dependencies with:
sudo apt-get install make gcc python-dev libbz2-dev
""", file=sys.stderr)
exit(1)
def clean_gemBS_tools():
process = subprocess.Popen(['make distclean'],shell=True,cwd='tools')
if process.wait() != 0:
print (""" Error Running cleaning. """,file=sys.stderr)
exit(1)
def _install_bundle(install_dir, inst):
"""Install compiled files to the GemBS installation Directory"""
if install_dir is None:
print("Unable to determine installation directory !")
exit(1)
gemBSbin_dir = os.path.join(install_dir, "gemBSbinaries")
if not os.path.exists(gemBSbin_dir):
os.mkdir(gemBSbin_dir)
# copy tools/bin
bins = ['gemBS_cat', 'readNameClean', 'md5_fasta', 'mextr', 'snpxtr']
for file in bins:
f = os.path.join('tools/bin', file)
if os.path.exists(f):
# print ("Copy binary: %s to %s" % (file, gemBSbin_dir))
result_file = os.path.join(gemBSbin_dir, file)
if os.path.exists(result_file):
os.remove(result_file)
shutil.copy(f, gemBSbin_dir)
os.chmod(result_file, 0o755)
if not (inst.minimal or inst.no_bscall):
# copy compiled bs_call tools
bins = [x for x in os.listdir("tools/bs_call/bin")]
for file in bins:
# print ("Copy binary: %s to %s" % (file, gemBSbin_dir))
result_file = os.path.join(gemBSbin_dir, file)
if os.path.exists(result_file):
os.remove(result_file)
shutil.copy(os.path.join("tools/bs_call/bin", file), gemBSbin_dir)
os.chmod(result_file, 0o755)
if not (inst.minimal or inst.no_gem3):
# copy compiled gem3 tools
bins = [x for x in os.listdir("tools/gem3-mapper/bin")]
for file in bins:
# print ("Copy binary: %s to %s" % (file, gemBSbin_dir))
result_file = os.path.join(install_dir, file)
if os.path.exists(result_file):
os.remove(result_file)
shutil.copy(os.path.join("tools/gem3-mapper/bin", file), gemBSbin_dir)
os.chmod(gemBSbin_dir, 0o755)
# copy samtools, bcftools and config files
bin_dir = os.path.join(install_dir, "bin")
lib_dir = os.path.join(install_dir, "lib")
etc_dir = os.path.join(install_dir, "etc")
config_dir = os.path.join(etc_dir, "gemBS_configs")
for dir in [bin_dir, lib_dir, config_dir]:
if not os.path.exists(dir):
os.makedirs(dir)
if not (inst.minimal or inst.no_samtools):
if os.path.exists("tools/samtools/samtools"):
# print ("Copy binary: samtools to {}".format(bin_dir))
shutil.copy("tools/samtools/samtools", bin_dir)
os.chmod(os.path.join(bin_dir, "samtools"), 0o755)
for htslib in glob.glob("tools/htslib"):
if os.path.isdir(htslib):
for file in ["htsfile", "tabix", "bgzip"]:
if os.path.exists(os.path.join(htslib,file)):
# print ("Copy binary: {} to {}".format(file, bin_dir))
shutil.copy(os.path.join(htslib,file), bin_dir)
os.chmod(os.path.join(bin_dir, file), 0o755)
for file in ["libhts.a", "libhts.so", "libhts.dylib"]:
if os.path.exists(os.path.join(htslib,file)):
# print ("Copy library: {} to {}".format(file, lib_dir))
shutil.copy(os.path.join(htslib,file), lib_dir)
os.chmod(os.path.join(lib_dir, file), 0o755)
if os.path.exists("tools/bcftools/bcftools"):
# print ("Copy binary: bcftools to {}".format(bin_dir))
shutil.copy("tools/bcftools/bcftools", bin_dir)
os.chmod(os.path.join(bin_dir, "bcftools"), 0o755)
files = [x for x in os.listdir("gemBS/etc")]
for file in files:
if os.path.isfile(os.path.join("gemBS/etc",file)):
# print ("Copy {} to {}".format(file, etc_dir))
shutil.copy(os.path.join("gemBS/etc",file), etc_dir)
os.chmod(os.path.join(etc_dir, file), 0o644)
files = [x for x in os.listdir("gemBS/etc/gemBS_configs")]
for file in files:
# print ("Copy {} to {}".format(file, config_dir))
shutil.copy(os.path.join("gemBS/etc/gemBS_configs",file), config_dir)
os.chmod(os.path.join(config_dir, file), 0o644)
# hack the setup tools installation
class install(_install):
_install.user_options.extend([
('no-samtools', None, "Do not install samtools"),
('no-gem3', None, "Do not install gem3 mapper"),
('no-bscall', None, "Do not install bscall"),
('minimal', None,
"Perform minimal install (equivalent to --no-samtools --no-gem3 --no-bscall)"),
('disable-cuda', None, "Do not build GPU support for GEM3 (default)"),
('enable-cuda', None, "Try to build GPU support for GEM3"),
])
_install.boolean_options.extend(['no-samtools','no-gem3','no-bscall','minimal'])
def initialize_options(self):
self.minimal = False
self.no_samtools = False
self.no_gem3 = False
self.no_bscall = False
self.disable_cuda = False
self.enable_cuda = False
_install.initialize_options(self)
def run(self):
options=['setup', '_bcftools', '_utils']
if not self.minimal:
if not self.no_samtools:
options.append('_samtools')
if not self.no_gem3:
options.append('gem3')
if not self.no_bscall:
options.append('_bs_call')
if not self.enable_cuda:
self.diable_cuda = True
compile_gemBS_tools(options, self.enable_cuda, self.disable_cuda)
_install.run(self)
# find target folder
install_dir = os.path.join(gemBS_install_dir, "gemBS")
_install_bundle(install_dir, self)
class install_lib(_install_lib):
def run(self):
# Store install_dir for future use
global gemBS_install_dir
gemBS_install_dir = self.install_dir
_install_lib.run(self)
def get_install_dir(self):
return self.install_dir
class install_scripts(_install_scripts):
def write_script(self, script_name, contents, mode="t", *ignored):
i = contents.find('__requires__')
if i >= 0:
j = contents.rfind('\n', 0, i)
if j >= 0:
contents = contents[:j+1] + "import sys\nsys.path.insert(0,'{}')\n".format(gemBS_install_dir) + contents[j+1:]
_install_scripts.write_script(self, script_name, contents, mode, *ignored)
# hack the setup tools cleaning
class clean(_clean):
def run(self):
_clean.run(self)
clean_gemBS_tools()
#_commands = {'install': install,'install_lib': install_lib, 'install_scripts': install_scripts, 'build_py': build_py,'clean':clean}
_commands = {'install': install,'install_lib': install_lib, 'install_scripts': install_scripts,'clean':clean}
setup(cmdclass=_commands,
name='gemBS',
version=__VERSION__,
description='Python application to perform the different steps involved in the Bisulphite Pipeline.',
author='Marcos Fernandez-Callejo, Santiago Marco-Sola, Simon Heath',
author_email='marcos.fernandez@cnag.crg.eu',
url='http://statgen.cnag.cat/gemBS/',
packages=['gemBS'],
package_data={"": [os.path.join("gemBS/gemBSbinaries", x) for x in ["readNameClean",
"gem-constructor",
"gem-indexer",
"gem-mapper",
"gem-retriever",
"bs_call",
"dbSNP_idx"
]]},
entry_points = {
'console_scripts': ['gemBS=gemBS.commands:gemBS_main'],
}
)
