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install.py
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install.py
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#!/usr/bin/env python
#
# Copyright (c) 2010-2015 Illumina, Inc.
# All rights reserved.
#
# This file is distributed under the simplified BSD license.
# The full text can be found here (and in LICENSE.txt in the root folder of
# this distribution):
#
# https://github.com/Illumina/licenses/blob/master/Simplified-BSD-License.txt
#
# hap.py installer:
#
# * checks dependencies
# * builds code
# * makes virtualenv
import os
import sys
import argparse
import subprocess
import tempfile
import shutil
import glob
import fnmatch
import multiprocessing
import urllib2
def check_python_version():
""" Check if the python version is sufficient """
if sys.version_info < (2, 7, 3):
raise Exception("You will need to run this with Python >= 2.7.3")
def create_python_environment(source_dir, args):
""" Create a Python runtime environment
:return: shebang with path to the python executable
"""
interp = args.python_interp
pyver = subprocess.check_output(interp +" -c \"import sys; print ','.join(map(str, list(sys.version_info["
"0:3])))\"", shell=True).strip().split(",")
pyver = tuple(map(int, pyver))
if pyver < (2, 7, 3):
raise Exception("Python >= 2.7.3 is required for installation.")
# system python -- just return interp
if args.python == "system":
return "#!" + interp
if not args.python_venv_dir:
raise Exception("Please specify a virtualenv target installation directory.")
if args.python_venv_dir_force:
try:
shutil.rmtree(args.python_venv_dir)
except:
pass
if os.path.exists(args.python_venv_dir) and not args.python_venv_dir_update:
raise Exception("The virtual environment directory already exists.")
virtualenv_tempdir = tempfile.mkdtemp(prefix="virtualenv", dir=args.scratch_path)
try:
ve_tgz = os.path.join(source_dir, "external", "virtualenv-12.0.7.tar.gz")
to_run = "cd %s && tar xzf %s" % (virtualenv_tempdir, ve_tgz)
print >>sys.stderr, to_run
subprocess.check_call(to_run, shell=True)
ve_exec = os.path.join(virtualenv_tempdir, "virtualenv-12.0.7", "virtualenv.py")
to_run = "%s -p %s %s" % (ve_exec, interp, args.python_venv_dir)
print >>sys.stderr, to_run
subprocess.check_call(to_run, shell=True)
finally:
if not args.keep_scratch:
try:
shutil.rmtree(virtualenv_tempdir)
except:
pass
# install requirements
ve_python = os.path.join(args.python_venv_dir, "bin", "python")
ve_pip = os.path.join(args.python_venv_dir, "bin", "pip")
deleteme = None
try:
cmds = [ve_pip, "install", "--no-cache-dir"]
if args.fix_cert:
response = urllib2.urlopen('http://curl.haxx.se/ca/cacert.pem')
certdata = response.read()
f = tempfile.NamedTemporaryFile(delete=False)
deleteme = f.name
f.write(certdata)
f.close()
cmds.insert(1, " --cert")
cmds.insert(2, deleteme)
for x in open(os.path.join(source_dir, "happy.requirements.txt")):
print >>sys.stderr, " ".join(cmds + [x])
subprocess.check_call(" ".join(cmds + [x]), shell=True)
finally:
if deleteme:
os.unlink(deleteme)
return "#!" + ve_python
def replace_shebang(filename, shebang):
""" Replace shebang line / reheader script files """
print >>sys.stderr, "Fixing shebang line in " + filename
with open(filename) as f:
lines = f.readlines()
with open(filename, "w") as f:
removed = False
print >> f, shebang
for i, l in enumerate(lines):
if not removed and l.startswith("#!") and i < 10:
removed = True
else:
f.write(l)
def build_external(source_dir, args):
""" Build hap.py external dependencies """
print >>sys.stderr, "Building external dependencies"
if args.boost:
boost_prefix = "BOOST_ROOT=%s " % args.boost
else:
boost_prefix = ""
setupscript = ""
if args.setup != "auto":
setupscript = " . %s && " % os.path.join(source_dir, "src", "sh", args.setup + "-setup.sh")
setupscript += boost_prefix
# remove builds
if args.external_build:
for x in ["zlib-1.2.8", "htslib", "bcftools", "samtools"]:
try:
shutil.rmtree(os.path.join(source_dir, "external", x))
print >>sys.stderr, "Deleted " + os.path.join(source_dir, "external", x)
except:
pass
to_run = "cd %s && %s ./make_dependencies.sh" % (os.path.join(source_dir, "external"),
setupscript)
print >>sys.stderr, to_run
subprocess.check_call(to_run, shell=True)
def build_haplotypes(source_dir, build_dir, args):
if args.boost:
boost_prefix = "BOOST_ROOT=%s " % args.boost
else:
boost_prefix = ""
config_command = "%s/configure.sh %s %s %s" % (source_dir, args.configuration, args.setup,
args.targetdir)
if args.sge:
config_command += " -DUSE_SGE=ON"
to_run = boost_prefix + "cd %s && %s %s" % (build_dir, boost_prefix, config_command)
print >>sys.stderr, to_run
subprocess.check_call(to_run, shell=True)
setupscript = ""
if args.setup != "auto":
setupscript = " . %s && " % os.path.join(source_dir, "src", "sh", args.setup + "-setup.sh")
setupscript += boost_prefix
to_run = setupscript + "cd %s && %s make -j%i" % (build_dir, setupscript, args.processes)
print >>sys.stderr, to_run
subprocess.check_call(to_run, shell=True)
to_run = setupscript + "cd %s && %s make -j%i install" % (build_dir, setupscript, args.processes)
print >>sys.stderr, to_run
subprocess.check_call(to_run, shell=True)
def test_haplotypes(source_dir, python_shebang, args):
""" Run the unit + integration tests
"""
to_run = "cd %s && %s" % (args.targetdir, os.path.join(source_dir, "src", "sh", "run_tests.sh"))
print >>sys.stderr, to_run
os.environ["PYTHON"] = python_shebang[2:]
subprocess.check_call(to_run, shell=True)
def main():
check_python_version()
source_dir = os.path.abspath(os.path.dirname(__file__))
parser = argparse.ArgumentParser("hap.py installer")
parser.add_argument("targetdir", help="Target installation directory")
parser.add_argument("--sge-mode",
dest="sge",
action="store_true",
default=False,
help="Enable SGE mode, which will require an additional command "
"line option \"--force-interactive\" to run interactively.")
parser.add_argument("--python",
dest="python",
choices=["system", "virtualenv"],
default="system",
help="Which Python to use in the installation. 'virtualenv' "
"will create a virtual environment in the folder "
"specified with --python-virtualenv-dir")
parser.add_argument("--python-interpreter", dest="python_interp",
default=sys.executable,
help="Python interpreter to use for the installed hap.py.")
parser.add_argument("--python-virtualenv-update", dest="python_venv_dir_update",
default=False, action="store_true",
help="Update virtualenv if it already exists.")
parser.add_argument("--python-virtualenv-force", dest="python_venv_dir_force",
default=False, action="store_true",
help="Force creating a virtualenv even if the target directory"
" already exists. USE WITH CARE, THIS WILL REMOVE THE "
"VIRTUALENV DIRECTORY!")
parser.add_argument("--python-virtualenv-dir", dest="python_venv_dir", default="",
help="Directory to install the virtualenv in.")
parser.add_argument("--pip-fix-cert", dest="fix_cert", default=False, action="store_true",
help="Download and use certificate file in case of Linux distributions"
" which have an outdated certificate file which makes pip fail.")
# C++ compile options
setups = map(lambda x: os.path.basename(x).replace("-setup.sh", ""),
glob.glob(os.path.join(source_dir, "src", "sh", "*-setup.sh")))
setups.insert(0, "auto")
parser.add_argument("--configuration", dest="configuration",
choices=["Debug", "Release", "RelWithDebInfo", "install"],
default="Release", help="Build configuration (use Release if unsure).")
parser.add_argument("--setup", dest="setup", choices=setups,
default="auto", help="Build setup (or auto to use system-wide packages).")
parser.add_argument("--boost-root", dest="boost",
help="Where to find Boost.", default="")
parser.add_argument("--scratch-path", dest="scratch_path",
help="Where to build.", default="/tmp")
parser.add_argument("--keep-scratch", dest="keep_scratch",
help="Keep the scratch folder.", default=False,
action="store_true")
parser.add_argument("--no-rebuild-external", dest="external_build", default=True,
action="store_false",
help="Don't rebuild external dependencies if not necessary.")
parser.add_argument("--build-processes", dest="processes",
default=multiprocessing.cpu_count(), type=int,
help="Number of parallel processes to use for building.")
parser.add_argument("--no-tests", dest="run_tests", default=True, action="store_false",
help="Disable unit tests")
args = parser.parse_args()
if args.python == "virtualenv" and not args.python_venv_dir:
raise Exception("Please specify a virtualenv target installation directory.")
if args.python_venv_dir and not args.python_venv_dir.startswith("/"):
args.python_venv_dir = args.targetdir
if "LD_LIBRARY_PATH" in os.environ or "DYLD_LIBRARY_PATH" in os.environ:
print >>sys.stderr, "WARNING: You have (DY)LD_LIBRARY_PATH set. Make sure these libraries are accessible " \
"in the same environment you will run in."
# fix dynamic linking
if "LD_LIBRARY_PATH" in os.environ:
os.environ["LD_RUN_PATH"] = os.environ["LD_LIBRARY_PATH"]
# check/make Python environment
python_shebang = create_python_environment(source_dir, args)
if args.boost and not os.path.exists(args.boost):
raise Exception("Boost directory doesn't exist.")
# build deps
build_external(source_dir, args)
# build hap.py
build_dir = tempfile.mkdtemp(prefix="build", dir=args.scratch_path)
try:
build_haplotypes(source_dir, build_dir, args)
finally:
if not args.keep_scratch:
shutil.rmtree(build_dir)
# reheader Python files
for root, dirnames, filenames in os.walk(args.targetdir):
for filename in fnmatch.filter(filenames, '*.py'):
replace_shebang(os.path.join(root, filename), python_shebang)
if args.run_tests:
test_haplotypes(source_dir, python_shebang, args)
if __name__ == '__main__':
main()