def __init__(self, zip_name, curl_exe=None, install_dir=None,
no_dependencies=False, prep_dependencies=False,
yes=False, me=False, add_symlinks=False):
print_to_screen(u"""{0} Rail-RNA v{1} Installer""".format(
u'\u2200', version_number)
)
if sys.platform in ['linux', 'linux2']:
if os.path.isfile('/mnt/var/lib/info/instance.json'):
# Assume an EMR cluster and prepend S3 download URLs
self.depends = dependency_urls.ec2_dependencies
else:
self.depends = dependency_urls.linux_dependencies
elif sys.platform == 'darwin':
self.depends = dependency_urls.mac_dependencies
else:
print_to_screen(
'Rail-RNA cannot be installed because it is not supported '
'by your OS. Currently supported OSes are Mac OS X and '
'Linux.'
)
sys.exit(1)
self.install_dir = install_dir
self.no_dependencies = no_dependencies
self.zip_name = os.path.abspath(zip_name)
self.curl_exe = curl_exe
log_dir = tempfile.mkdtemp()
self.log_file = os.path.join(log_dir, 'rail-rna_install.log')
self.log_stream = open(self.log_file, 'w')
self.finished = False
register_cleanup(remove_temporary_directories, [log_dir])
self.yes = yes or me
self.me = me
self.prep_dependencies = prep_dependencies
self.add_symlinks = add_symlinks
def __init__(self, zip_name, curl_exe=None, install_dir=None,
no_dependencies=False, prep_dependencies=False,
yes=False, me=False, add_symlinks=False):
print_to_screen(u"""{0} Rail-RNA v{1} Installer""".format(
u'\u2200', version_number)
)
if sys.platform in ['linux', 'linux2']:
if os.path.isfile('/mnt/var/lib/info/instance.json'):
# Assume an EMR cluster and prepend S3 download URLs
self.depends = dependency_urls.ec2_dependencies
else:
self.depends = dependency_urls.linux_dependencies
elif sys.platform == 'darwin':
self.depends = dependency_urls.mac_dependencies
else:
print_to_screen(
'Rail-RNA cannot be installed because it is not supported '
'by your OS. Currently supported OSes are Mac OS X and '
'Linux.'
)
sys.exit(1)
self.install_dir = install_dir
self.no_dependencies = no_dependencies
self.zip_name = os.path.abspath(zip_name)
self.curl_exe = curl_exe
log_dir = tempfile.mkdtemp()
self.log_file = os.path.join(log_dir, 'rail-rna_install.log')
self.log_stream = open(self.log_file, 'w')
self.finished = False
register_cleanup(remove_temporary_directories, [log_dir])
self.yes = yes or me
self.me = me
self.prep_dependencies = prep_dependencies
self.add_symlinks = add_symlinks
def _bail(self):
""" Copy log to some temporary dir and GTFO. """
new_log_file = os.path.join(tempfile.mkdtemp(),
'rail-rna_installer.log')
shutil.copyfile(self.log_file, new_log_file)
print_to_screen('Installation log may be found at %s.' % new_log_file)
sys.exit(1)
def _bail(self):
""" Copy log to some temporary dir and GTFO. """
new_log_file = os.path.join(tempfile.mkdtemp(),
'rail-rna_installer.log')
shutil.copyfile(self.log_file, new_log_file)
print_to_screen('Installation log may be found at %s.' % new_log_file)
sys.exit(1)
def __exit__(self, type, value, traceback):
try:
self.log_stream.close()
except:
pass
if self.finished:
# Stuck around, so bailing did not happen; put in rail dir
assert hasattr(self, 'final_install_dir')
new_log_file = os.path.join(self.final_install_dir,
'rail-rna_installer.log')
shutil.copyfile(self.log_file, new_log_file)
print_to_screen('Installation log may be found at %s.'
% new_log_file)
print_to_screen('*Before running any commands below, enter '
'"source ~/.bash_profile".*')
if self.installed_aws:
print_to_screen('Configure the AWS CLI by running '
'"aws configure". Afterwards, run '
'"aws emr create-default-roles" '
'to use default IAM roles on Amazon '
'Elastic MapReduce. To learn more '
'about IAM roles, visit http://docs.'
'aws.amazon.com/IAM/latest/UserGuide/'
'roles-toplevel.html .')
print_to_screen('Start using Rail by entering "rail-rna".')
def __exit__(self, type, value, traceback):
try:
self.log_stream.close()
except:
pass
if self.finished:
# Stuck around, so bailing did not happen; put in rail dir
assert hasattr(self, 'final_install_dir')
new_log_file = os.path.join(self.final_install_dir,
'rail-rna_installer.log')
shutil.copyfile(self.log_file, new_log_file)
print_to_screen('Installation log may be found at %s.'
% new_log_file)
if self.local:
print_to_screen('*Before running any commands below, enter '
'"source ~/.bash_profile".*')
if self.installed_aws:
print_to_screen('Configure the AWS CLI by running '
'"aws configure". Afterwards, run '
'"aws emr create-default-roles" '
'to use default IAM roles on Amazon '
'Elastic MapReduce. To learn more '
'about IAM roles, visit http://docs.'
'aws.amazon.com/IAM/latest/UserGuide/'
'roles-toplevel.html .')
print_to_screen('Start using Rail by entering "rail-rna".')
def _bail(self):
""" Copy log to some temporary dir and GTFO. """
new_log_file = os.path.join(tempfile.mkdtemp(),
'rail-rna_installer.log')
shutil.copyfile(self.log_file, new_log_file)
if self.print_log_on_error:
print_to_screen('Installation log (also at %s):' % new_log_file)
print_to_screen('===')
with open(new_log_file, 'r') as log_fh:
for ln in log_fh:
print_to_screen(ln.rstrip())
print_to_screen('===')
else:
print_to_screen('Installation log may be found at %s.' % new_log_file)
sys.exit(1)
def _print_to_screen_and_log(self, message, **kwargs):
print >>self.log_stream, message
print_to_screen(message, **kwargs)
def install(self):
""" Installs Rail-RNA and all its dependencies. """
if not self.no_dependencies and self.curl_exe is None:
self.curl_exe = which('curl')
if self.curl_exe is None:
print_to_screen('Rail-RNA\'s installer requires Curl if '
'dependencies are to be installed. '
'Download it at '
'http://curl.haxx.se/download.html and use '
'--curl to specify its path, or '
'disable installing dependencies with '
'--no-dependencies.')
sys.exit(1)
if self._yes_no_query(
'Rail-RNA can be installed for all users or just the '
'current user.\n * Install for all users?',
answer=(None if not self.yes else (self.yes and not self.me))
):
if os.getuid():
print_to_screen('Rerun with sudo privileges to install '
'for all users.')
sys.exit(0)
install_dir = '/usr/local'
self.local = False
else:
install_dir = os.path.abspath(os.path.expanduser('~/'))
self.local = True
bin_dir = os.path.join(install_dir, 'bin')
rail_exe = os.path.join(bin_dir, 'rail-rna')
if self.install_dir is None:
self.final_install_dir = os.path.join(install_dir, 'raildotbio')
else:
# User specified an installation directory
self.final_install_dir = self.install_dir
# Install in a temporary directory first, then move to final dest
temp_install_dir = tempfile.mkdtemp()
register_cleanup(remove_temporary_directories, [temp_install_dir])
if os.path.exists(self.final_install_dir):
if self._yes_no_query(
('The installation path {dir} already exists.\n '
'* Overwrite {dir}?').format(dir=self.final_install_dir)
):
try:
shutil.rmtree(self.final_install_dir)
except OSError:
# Handle this later if directory creation fails
pass
try:
os.remove(self.final_install_dir)
except OSError:
pass
else:
print_to_screen(
'Specify a different installation directory with '
'--install-dir.'
)
sys.exit(0)
self._print_to_screen_and_log('[Installing] Extracting Rail-RNA...',
newline=False,
carriage_return=True)
try:
os.makedirs(self.final_install_dir)
except OSError as e:
self._print_to_screen_and_log(
('Problem encountered trying to create '
'directory %s for installation. May need '
'sudo permissions.') % self.final_install_dir
)
self._bail()
else:
# So it's possible to move temp installation dir there
os.rmdir(self.final_install_dir)
pass
with cd(temp_install_dir):
with zipfile.ZipFile(self.zip_name) as zip_object:
zip_object.extractall('./rail-rna')
if not self.no_dependencies:
self._grab_and_explode(self.depends['pypy'], 'PyPy')
self._grab_and_explode(self.depends['sra_tools'], 'SRA Tools')
if not self.prep_dependencies:
self._grab_and_explode(self.depends['bowtie1'], 'Bowtie 1')
self._grab_and_explode(self.depends['bowtie2'], 'Bowtie 2')
self._grab_and_explode(self.depends['bedgraphtobigwig'],
'BedGraphToBigWig')
self._grab_and_explode(self.depends['samtools'],
'SAMTools')
if not self.prep_dependencies and not self.no_dependencies:
# Have to make SAMTools (annoying; maybe change this)
samtools_dir = os.path.join(temp_install_dir,
self.depends['samtools'][0].rpartition('/')[2][:-8]
)
with cd(samtools_dir):
'''Make sure unistd.h is #included cram_io.c ... it's some
bug in some SAMTools that prevents compilation on
langmead-fs1, which may be a general problem with
portability. See https://github.com/samtools/htslib/commit/
0ec5202de5691b27917ce828a9d24c9c729a9b81'''
cram_io_file = os.path.join(glob.glob('./htslib-*')[0],
'cram', 'cram_io.c')
with open(cram_io_file) as cram_io_stream:
all_cram_io = cram_io_stream.read()
if '<unistd.h>' not in all_cram_io:
with open(cram_io_file, 'w') as cram_io_out_stream:
cram_io_out_stream.write(all_cram_io.replace(
'#include <string.h>',
'#include <string.h>\n#include <unistd.h>'
))
makefile = 'Makefile'
with open(makefile) as makefile_stream:
all_makefile = makefile_stream.read()
with open(makefile, 'w') as makefile_stream:
makefile_stream.write(
all_makefile.replace(
'-D_CURSES_LIB=1', '-D_CURSES_LIB=0'
).replace('LIBCURSES=','#LIBCURSES=')
)
# Make on all but one cylinder
thread_count = max(1, multiprocessing.cpu_count() - 1)
samtools_command = ['make', '-j%d' % thread_count]
self._print_to_screen_and_log(
'[Installing] Making SAMTools...',
newline=False,
carriage_return=True
)
try:
subprocess.check_output(samtools_command,
stderr=self.log_stream)
except subprocess.CalledProcessError as e:
self._print_to_screen_and_log(
('Error encountered making SAMTools; exit '
'code was %d; command invoked was "%s".') %
(e.returncode, ' '.join(samtools_command))
)
self._bail()
samtools = os.path.join(self.final_install_dir,
self.depends['samtools'][0].rpartition('/')[2][:-8],
'samtools')
bowtie1_base = '-'.join(
self.depends['bowtie1'][0].rpartition(
'/'
)[2].split('-')[:2]
)
bowtie1 = os.path.join(self.final_install_dir,
bowtie1_base, 'bowtie')
bowtie1_build = os.path.join(self.final_install_dir,
bowtie1_base, 'bowtie-build')
bowtie2_base = '-'.join(
self.depends['bowtie2'][0].rpartition(
'/'
)[2].split('-')[:2]
)
bowtie2 = os.path.join(self.final_install_dir,
bowtie2_base, 'bowtie2')
bowtie2_build = os.path.join(self.final_install_dir,
bowtie2_base, 'bowtie2-build')
bedgraphtobigwig = os.path.join(
self.final_install_dir,
'bedGraphToBigWig'
)
else:
bowtie1 = bowtie1_build = bowtie2 = bowtie2_build \
= bedgraphtobigwig = samtools = 'None'
if self.no_dependencies:
pypy = 'None'
fastq_dump = 'None'
vdb_config = 'None'
else:
pypy = os.path.join(self.final_install_dir,
self.depends['pypy'][0].rpartition(
'/'
)[2][:-8], 'bin', 'pypy'
)
fastq_dump = os.path.join(self.final_install_dir,
self.depends['sra_tools'][0].rpartition(
'/'
)[2][:-7], 'bin', 'fastq-dump'
)
vdb_config = os.path.join(self.final_install_dir,
self.depends['sra_tools'][0].rpartition(
'/'
)[2][:-7], 'bin', 'vdb-config'
)
# Write paths to exe_paths
with open(
os.path.join(temp_install_dir, 'rail-rna',
'exe_paths.py'), 'w'
) as exe_paths_stream:
print >>exe_paths_stream, (
"""\"""
exe_paths.py
Part of Rail-RNA
Defines default paths of Rail-RNA's executable dependencies. Set a given
variable equal to None if the default path should be in PATH.
\"""
pypy = {pypy}
aws = None
curl = None
sort = None
bowtie1 = {bowtie1}
bowtie1_build = {bowtie1_build}
bowtie2 = {bowtie2}
bowtie2_build = {bowtie2_build}
samtools = {samtools}
bedgraphtobigwig = {bedgraphtobigwig}
fastq_dump = {fastq_dump}
vdb_config = {vdb_config}
"""
).format(pypy=self._quote(pypy), bowtie1=self._quote(bowtie1),
bowtie1_build=self._quote(bowtie1_build),
bowtie2=self._quote(bowtie2),
bowtie2_build=self._quote(bowtie2_build),
samtools=self._quote(samtools),
bedgraphtobigwig=self._quote(bedgraphtobigwig),
fastq_dump=self._quote(fastq_dump),
vdb_config=self._quote(vdb_config))
# Move to final directory
try:
shutil.move(temp_install_dir, self.final_install_dir)
except Exception as e:
self._print_to_screen_and_log(('Problem "%s" encountered moving '
'temporary installation directory '
'%s to final destination %s.') % (
e,
temp_install_dir,
self.final_install_dir
))
self._bail()
# Create shell-script executable
try:
os.makedirs(bin_dir)
except Exception as e:
if not os.path.isdir(bin_dir):
self._print_to_screen_and_log(('Problem "%s" encountered '
'creating directory %s.') % (
e,
bin_dir
)
)
self._bail()
install_dir_replacement = os.path.join(
self.final_install_dir, 'rail-rna'
)
with open(rail_exe, 'w') as rail_exe_stream:
print >>rail_exe_stream, (
"""#!/usr/bin/env bash
{python_executable} {install_dir} $@
"""
).format(python_executable=sys.executable,
install_dir=install_dir_replacement)
if self.local:
'''Have to add Rail to PATH. Do this in bashrc and bash_profile
contingent on whether it's present already because of
inconsistent behavior across Mac OS and Linux distros.'''
to_print = (
"""
## Rail-RNA additions
if [ -d "{bin_dir}" ] && [[ ":$PATH:" != *":{bin_dir}:"* ]]; then
PATH="${{PATH:+"$PATH:"}}{bin_dir}"
fi
export RAILDOTBIO={install_dir}
## End Rail-RNA additions
"""
).format(bin_dir=bin_dir,
install_dir=install_dir_replacement)
else:
# Just define raildotbio directory
to_print = (
"""
## Rail-RNA addition
export RAILDOTBIO={install_dir}
## End Rail-RNA addition
"""
).format(bin_dir=bin_dir,
install_dir=install_dir_replacement)
import mmap
bashrc = os.path.expanduser('~/.bashrc')
bash_profile = os.path.expanduser('~/.bash_profile')
try:
with open(bashrc) as bashrc_stream:
mmapped = mmap.mmap(bashrc_stream.fileno(), 0,
access=mmap.ACCESS_READ)
if mmapped.find(to_print) == -1:
print_to_bashrc = True
else:
print_to_bashrc = False
except (IOError, ValueError):
# No file
print_to_bashrc = True
try:
with open(bash_profile) as bash_profile_stream:
mmapped = mmap.mmap(bash_profile_stream.fileno(), 0,
access=mmap.ACCESS_READ)
if mmapped.find(to_print) == -1:
print_to_bash_profile = True
else:
print_to_bash_profile = False
except (IOError, ValueError):
# No file
print_to_bash_profile = True
if print_to_bashrc:
with open(bashrc, 'a') as bashrc_stream:
print >>bashrc_stream, to_print
if print_to_bash_profile:
with open(bash_profile, 'a') as bash_profile_stream:
print >>bash_profile_stream, to_print
# Set 755 permissions across Rail's dirs and 644 across files
dir_command = ['find', self.final_install_dir, '-type', 'd',
'-exec', 'chmod', '755', '{}', ';']
file_command = ['find', self.final_install_dir, '-type', 'f',
'-exec', 'chmod', '644', '{}', ';']
try:
subprocess.check_output(dir_command,
stderr=self.log_stream)
except subprocess.CalledProcessError as e:
self._print_to_screen_and_log(
('Error encountered changing directory '
'permissions; exit code was %d; command invoked '
'was "%s".') %
(e.returncode, ' '.join(dir_command))
)
self._bail()
try:
subprocess.check_output(file_command,
stderr=self.log_stream)
except subprocess.CalledProcessError as e:
self._print_to_screen_and_log(
('Error encountered changing file '
'permissions; exit code was %d; command invoked '
'was "%s".') %
(e.returncode, ' '.join(file_command))
)
self._bail()
# Go back and set 755 permissions for executables
os.chmod(rail_exe, 0755)
if not self.no_dependencies:
os.chmod(pypy, 0755)
os.chmod(fastq_dump, 0755)
os.chmod(vdb_config, 0755)
if not self.prep_dependencies:
for program in [bowtie1, bowtie1_build, bowtie2, bowtie2_build,
samtools, bedgraphtobigwig]:
os.chmod(program, 0755)
# Also for misc. Bowtie executables
for program in glob.glob(
os.path.join(os.path.dirname(bowtie1), 'bowtie-*')
):
os.chmod(program, 0755)
for program in glob.glob(
os.path.join(os.path.dirname(bowtie2), 'bowtie2-*')
):
os.chmod(program, 0755)
if self.add_symlinks:
# Write appropriate symlinks
self._add_symlink_to_exe(pypy)
self._add_symlink_to_exe(fastq_dump)
self._add_symlink_to_exe(vdb_config)
if not self.prep_dependencies:
for program in [bowtie1, bowtie1_build, bowtie2,
bowtie2_build, samtools, bedgraphtobigwig]:
self._add_symlink_to_exe(program)
self._print_to_screen_and_log('Installed Rail-RNA.')
# IPython much?
try:
import IPython
except ImportError:
# Guess not
if self._yes_no_query(
'IPython is not installed but required for Rail-RNA to '
'work in its "parallel" mode.\n'
' * Install IPython now?'
):
temp_ipython_install_dir = tempfile.mkdtemp()
register_cleanup(remove_temporary_directories,
[temp_ipython_install_dir])
with cd(temp_ipython_install_dir):
self._grab_and_explode(self.depends['ipython'], 'IPython')
setup_dir = os.path.dirname(find('setup.py', './'))
with cd(setup_dir):
ipython_command = [
sys.executable, 'setup.py', 'install',
]
if self.local:
ipython_command.append('--user')
try:
subprocess.check_output(ipython_command,
stderr=self.log_stream)
except subprocess.CalledProcessError as e:
self._print_to_screen_and_log(
('Error encountered installing IPython; exit '
'code was %d; command invoked was "%s".') %
(e.returncode, ' '.join(ipython_command))
)
self._bail()
install_aws = (not self.no_dependencies and not which('aws'))
self.installed_aws = False
if install_aws and self._yes_no_query(
'AWS CLI is not installed but required for Rail-RNA to work '
'in its "elastic" mode, on Amazon Elastic MapReduce.\n'
' * Install AWS CLI now?'
):
temp_aws_install_dir = tempfile.mkdtemp()
register_cleanup(remove_temporary_directories,
[temp_aws_install_dir])
with cd(temp_aws_install_dir):
self._grab_and_explode(self.depends['aws_cli'], 'AWS CLI')
os.chmod('./awscli-bundle/install', 0755)
if self.local:
# Local install
aws_command = ['./awscli-bundle/install', '-b',
os.path.join(bin_dir, 'aws'),
'-i', os.path.abspath(
os.path.expanduser('~/.local/lib/aws')
)]
else:
# All users
aws_command = ['./awscli-bundle/install',
'-i', '/usr/local/aws',
'-b', '/usr/local/bin/aws']
try:
subprocess.check_output(aws_command,
stderr=self.log_stream)
except (OSError, subprocess.CalledProcessError) as e:
self._print_to_screen_and_log(
('Error encountered installing AWS CLI; exit '
'code was %d; command invoked was "%s".') %
(e.returncode, ' '.join(aws_command))
)
self._bail()
self.installed_aws = True
elif install_aws:
print_to_screen('Visit http://docs.aws.amazon.com/cli/latest/'
'userguide/installing.html to install the '
'AWS CLI later.')
self.finished = True
def _print_to_screen_and_log(self, message, **kwargs):
print >>self.log_stream, message
print_to_screen(message, **kwargs)
def install(self):
""" Installs Rail-RNA and all its dependencies. """
if not self.no_dependencies and self.curl_exe is None:
self.curl_exe = which('curl')
if self.curl_exe is None:
print_to_screen('Rail-RNA\'s installer requires Curl if '
'dependencies are to be installed. '
'Download it at '
'http://curl.haxx.se/download.html and use '
'--curl to specify its path, or '
'disable installing dependencies with '
'--no-dependencies.')
sys.exit(1)
if self._yes_no_query(
'Rail-RNA can be installed for all users or just the '
'current user.\n * Install for all users?',
answer=(None if not self.yes else (self.yes and not self.me))
):
if os.getuid():
print_to_screen('Rerun with sudo privileges to install '
'for all users.')
sys.exit(0)
install_dir = '/usr/local'
self.local = False
else:
install_dir = os.path.abspath(os.path.expanduser('~/'))
self.local = True
bin_dir = os.path.join(install_dir, 'bin')
rail_exe = os.path.join(bin_dir, 'rail-rna')
if self.install_dir is None:
self.final_install_dir = os.path.join(install_dir, 'raildotbio')
else:
# User specified an installation directory
self.final_install_dir = self.install_dir
# Install in a temporary directory first, then move to final dest
temp_install_dir = tempfile.mkdtemp()
register_cleanup(remove_temporary_directories, [temp_install_dir])
if os.path.exists(self.final_install_dir):
if self._yes_no_query(
('The installation path {dir} already exists.\n '
'* Overwrite {dir}?').format(dir=self.final_install_dir)
):
try:
shutil.rmtree(self.final_install_dir)
except OSError:
# Handle this later if directory creation fails
pass
try:
os.remove(self.final_install_dir)
except OSError:
pass
else:
print_to_screen(
'Specify a different installation directory with '
'--install-dir.'
)
sys.exit(0)
self._print_to_screen_and_log('[Installing] Extracting Rail-RNA...',
newline=False,
carriage_return=True)
try:
os.makedirs(self.final_install_dir)
except OSError as e:
self._print_to_screen_and_log(
('Problem encountered trying to create '
'directory %s for installation. May need '
'sudo permissions.') % self.final_install_dir
)
self._bail()
else:
# So it's possible to move temp installation dir there
os.rmdir(self.final_install_dir)
pass
with cd(temp_install_dir):
with zipfile.ZipFile(self.zip_name) as zip_object:
zip_object.extractall('./rail-rna')
if not self.no_dependencies:
self._grab_and_explode(self.depends['pypy'], 'PyPy')
self._grab_and_explode(self.depends['sra_tools'], 'SRA Tools')
if not self.prep_dependencies:
self._grab_and_explode(self.depends['bowtie1'], 'Bowtie 1')
self._grab_and_explode(self.depends['bowtie2'], 'Bowtie 2')
self._grab_and_explode(self.depends['bedgraphtobigwig'],
'BedGraphToBigWig')
self._grab_and_explode(self.depends['samtools'],
'SAMTools')
if not self.prep_dependencies and not self.no_dependencies:
# Have to make SAMTools (annoying; maybe change this)
samtools_dir = os.path.join(temp_install_dir,
self.depends['samtools'][0].rpartition('/')[2][:-8]
)
with cd(samtools_dir):
'''Make sure unistd.h is #included cram_io.c ... it's some
bug in some SAMTools that prevents compilation on
langmead-fs1, which may be a general problem with
portability. See https://github.com/samtools/htslib/commit/
0ec5202de5691b27917ce828a9d24c9c729a9b81'''
cram_io_file = os.path.join(glob.glob('./htslib-*')[0],
'cram', 'cram_io.c')
with open(cram_io_file) as cram_io_stream:
all_cram_io = cram_io_stream.read()
if '<unistd.h>' not in all_cram_io:
with open(cram_io_file, 'w') as cram_io_out_stream:
cram_io_out_stream.write(all_cram_io.replace(
'#include <string.h>',
'#include <string.h>\n#include <unistd.h>'
))
makefile = 'Makefile'
with open(makefile) as makefile_stream:
all_makefile = makefile_stream.read()
with open(makefile, 'w') as makefile_stream:
makefile_stream.write(
all_makefile.replace(
'-D_CURSES_LIB=1', '-D_CURSES_LIB=0'
).replace('LIBCURSES=','#LIBCURSES=')
)
# Make on all but one cylinder
thread_count = max(1, multiprocessing.cpu_count() - 1)
samtools_command = ['make', '-j%d' % thread_count]
self._print_to_screen_and_log(
'[Installing] Making SAMTools...',
newline=False,
carriage_return=True
)
try:
subprocess.check_output(samtools_command,
stderr=self.log_stream)
except subprocess.CalledProcessError as e:
self._print_to_screen_and_log(
('Error encountered making SAMTools; exit '
'code was %d; command invoked was "%s".') %
(e.returncode, ' '.join(samtools_command))
)
self._bail()
samtools = os.path.join(self.final_install_dir,
self.depends['samtools'][0].rpartition('/')[2][:-8],
'samtools')
bowtie1_base = '-'.join(
self.depends['bowtie1'][0].rpartition(
'/'
)[2].split('-')[:2]
)
bowtie1 = os.path.join(self.final_install_dir,
bowtie1_base, 'bowtie')
bowtie1_build = os.path.join(self.final_install_dir,
bowtie1_base, 'bowtie-build')
bowtie2_base = '-'.join(
self.depends['bowtie2'][0].rpartition(
'/'
)[2].split('-')[:2]
)
bowtie2 = os.path.join(self.final_install_dir,
bowtie2_base, 'bowtie2')
bowtie2_build = os.path.join(self.final_install_dir,
bowtie2_base, 'bowtie2-build')
bedgraphtobigwig = os.path.join(
self.final_install_dir,
'bedGraphToBigWig'
)
else:
bowtie1 = bowtie1_build = bowtie2 = bowtie2_build \
= bedgraphtobigwig = samtools = 'None'
if self.no_dependencies:
pypy = 'None'
fastq_dump = 'None'
vdb_config = 'None'
else:
pypy = os.path.join(self.final_install_dir,
self.depends['pypy'][0].rpartition(
'/'
)[2][:-8], 'bin', 'pypy'
)
fastq_dump = os.path.join(self.final_install_dir,
self.depends['sra_tools'][0].rpartition(
'/'
)[2][:-7], 'bin', 'fastq-dump'
)
vdb_config = os.path.join(self.final_install_dir,
self.depends['sra_tools'][0].rpartition(
'/'
)[2][:-7], 'bin', 'vdb-config'
)
# Write paths to exe_paths
with open(
os.path.join(temp_install_dir, 'rail-rna',
'exe_paths.py'), 'w'
) as exe_paths_stream:
print >>exe_paths_stream, (
"""\"""
exe_paths.py
Part of Rail-RNA
Defines default paths of Rail-RNA's executable dependencies. Set a given
variable equal to None if the default path should be in PATH.
\"""
pypy = {pypy}
aws = None
curl = None
sort = None
bowtie1 = {bowtie1}
bowtie1_build = {bowtie1_build}
bowtie2 = {bowtie2}
bowtie2_build = {bowtie2_build}
samtools = {samtools}
bedgraphtobigwig = {bedgraphtobigwig}
fastq_dump = {fastq_dump}
vdb_config = {vdb_config}
"""
).format(pypy=self._quote(pypy), bowtie1=self._quote(bowtie1),
bowtie1_build=self._quote(bowtie1_build),
bowtie2=self._quote(bowtie2),
bowtie2_build=self._quote(bowtie2_build),
samtools=self._quote(samtools),
bedgraphtobigwig=self._quote(bedgraphtobigwig),
fastq_dump=self._quote(fastq_dump),
vdb_config=self._quote(vdb_config))
# Move to final directory
try:
shutil.move(temp_install_dir, self.final_install_dir)
except Exception as e:
self._print_to_screen_and_log(('Problem "%s" encountered moving '
'temporary installation directory '
'%s to final destination %s.') % (
e,
temp_install_dir,
self.final_install_dir
))
self._bail()
# Create shell-script executable
try:
os.makedirs(bin_dir)
except Exception as e:
if not os.path.isdir(bin_dir):
self._print_to_screen_and_log(('Problem "%s" encountered '
'creating directory %s.') % (
e,
bin_dir
)
)
self._bail()
with open(rail_exe, 'w') as rail_exe_stream:
print >>rail_exe_stream, (
"""#!/usr/bin/env bash
{python_executable} {install_dir} $@
"""
).format(python_executable=sys.executable,
install_dir=os.path.join(
self.final_install_dir, 'rail-rna'
))
if self.local:
'''Have to add Rail to PATH. Do this in bashrc and bash_profile
contingent on whether it's present already because of
inconsistent behavior across Mac OS and Linux distros.'''
to_print = (
"""
## Rail-RNA additions
if [ -d "{bin_dir}" ] && [[ ":$PATH:" != *":{bin_dir}:"* ]]; then
PATH="${{PATH:+"$PATH:"}}{bin_dir}"
fi
## End Rail-RNA additions
"""
).format(bin_dir=bin_dir)
import mmap
bashrc = os.path.expanduser('~/.bashrc')
bash_profile = os.path.expanduser('~/.bash_profile')
try:
with open(bashrc) as bashrc_stream:
mmapped = mmap.mmap(bashrc_stream.fileno(), 0,
access=mmap.ACCESS_READ)
if mmapped.find(to_print) == -1:
print_to_bashrc = True
else:
print_to_bashrc = False
except (IOError, ValueError):
# No file
print_to_bashrc = True
try:
with open(bash_profile) as bash_profile_stream:
mmapped = mmap.mmap(bash_profile_stream.fileno(), 0,
access=mmap.ACCESS_READ)
if mmapped.find(to_print) == -1:
print_to_bash_profile = True
else:
print_to_bash_profile = False
except (IOError, ValueError):
# No file
print_to_bash_profile = True
if print_to_bashrc:
with open(bashrc, 'a') as bashrc_stream:
print >>bashrc_stream, to_print
if print_to_bash_profile:
with open(bash_profile, 'a') as bash_profile_stream:
print >>bash_profile_stream, to_print
# Set 755 permissions across Rail's dirs and 644 across files
dir_command = ['find', self.final_install_dir, '-type', 'd',
'-exec', 'chmod', '755', '{}', ';']
file_command = ['find', self.final_install_dir, '-type', 'f',
'-exec', 'chmod', '644', '{}', ';']
try:
subprocess.check_output(dir_command,
stderr=self.log_stream)
except subprocess.CalledProcessError as e:
self._print_to_screen_and_log(
('Error encountered changing directory '
'permissions; exit code was %d; command invoked '
'was "%s".') %
(e.returncode, ' '.join(dir_command))
)
self._bail()
try:
subprocess.check_output(file_command,
stderr=self.log_stream)
except subprocess.CalledProcessError as e:
self._print_to_screen_and_log(
('Error encountered changing file '
'permissions; exit code was %d; command invoked '
'was "%s".') %
(e.returncode, ' '.join(file_command))
)
self._bail()
# Go back and set 755 permissions for executables
os.chmod(rail_exe, 0755)
if not self.no_dependencies:
os.chmod(pypy, 0755)
os.chmod(fastq_dump, 0755)
os.chmod(vdb_config, 0755)
if not self.prep_dependencies:
for program in [bowtie1, bowtie1_build, bowtie2, bowtie2_build,
samtools, bedgraphtobigwig]:
os.chmod(program, 0755)
# Also for misc. Bowtie executables
for program in glob.glob(
os.path.join(os.path.dirname(bowtie1), 'bowtie-*')
):
os.chmod(program, 0755)
for program in glob.glob(
os.path.join(os.path.dirname(bowtie2), 'bowtie2-*')
):
os.chmod(program, 0755)
if self.add_symlinks:
# Write appropriate symlinks
self._add_symlink_to_exe(pypy)
self._add_symlink_to_exe(fastq_dump)
self._add_symlink_to_exe(vdb_config)
if not self.prep_dependencies:
for program in [bowtie1, bowtie1_build, bowtie2,
bowtie2_build, samtools, bedgraphtobigwig]:
self._add_symlink_to_exe(program)
self._print_to_screen_and_log('Installed Rail-RNA.')
# IPython much?
try:
import IPython
except ImportError:
# Guess not
if self._yes_no_query(
'IPython is not installed but required for Rail-RNA to '
'work in its "parallel" mode.\n'
' * Install IPython now?'
):
temp_ipython_install_dir = tempfile.mkdtemp()
register_cleanup(remove_temporary_directories,
[temp_ipython_install_dir])
with cd(temp_ipython_install_dir):
self._grab_and_explode(self.depends['ipython'], 'IPython')
setup_dir = os.path.dirname(find('setup.py', './'))
with cd(setup_dir):
ipython_command = [
sys.executable, 'setup.py', 'install',
]
if self.local:
ipython_command.append('--user')
try:
subprocess.check_output(ipython_command,
stderr=self.log_stream)
except subprocess.CalledProcessError as e:
self._print_to_screen_and_log(
('Error encountered installing IPython; exit '
'code was %d; command invoked was "%s".') %
(e.returncode, ' '.join(ipython_command))
)
self._bail()
install_aws = (not self.no_dependencies and not which('aws'))
self.installed_aws = False
if install_aws and self._yes_no_query(
'AWS CLI is not installed but required for Rail-RNA to work '
'in its "elastic" mode, on Amazon Elastic MapReduce.\n'
' * Install AWS CLI now?'
):
temp_aws_install_dir = tempfile.mkdtemp()
register_cleanup(remove_temporary_directories,
[temp_aws_install_dir])
with cd(temp_aws_install_dir):
self._grab_and_explode(self.depends['aws_cli'], 'AWS CLI')
os.chmod('./awscli-bundle/install', 0755)
if self.local:
# Local install
aws_command = ['./awscli-bundle/install', '-b',
os.path.join(bin_dir, 'aws'),
'-i', os.path.abspath(
os.path.expanduser('~/.local/lib/aws')
)]
else:
# All users
aws_command = ['./awscli-bundle/install',
'-i', '/usr/local/aws',
'-b', '/usr/local/bin/aws']
try:
subprocess.check_output(aws_command,
stderr=self.log_stream)
except (OSError, subprocess.CalledProcessError) as e:
self._print_to_screen_and_log(
('Error encountered installing AWS CLI; exit '
'code was %d; command invoked was "%s".') %
(e.returncode, ' '.join(aws_command))
)
self._bail()
self.installed_aws = True
elif install_aws:
print_to_screen('Visit http://docs.aws.amazon.com/cli/latest/'
'userguide/installing.html to install the '
'AWS CLI later.')
self.finished = True