--- /dev/null
+"""
+Generate settings for the Django Application.
+
+To make it easier to customize the application the settings can be
+defined in a configuration file read by ConfigParser.
+
+The options understood by this module are (with their defaults):
+
+ [frontend]
+ email_host=localhost
+ email_port=25
+ database_engine=sqlite3
+ database_name=/path/to/db
+
+ [admins]
+ #name1=email1
+
+ [allowed_hosts]
+ #name1=ip
+ localhost=127.0.0.1
+
+ [allowed_analysis_hosts]
+ #name1=ip
+ localhost=127.0.0.1
+
+"""
+import ConfigParser
+import os
+import shlex
+
+# make epydoc happy
+__docformat__ = "restructuredtext en"
+
+def options_to_list(options, dest, section_name, option_name):
+ """
+ Load a options from section_name and store in a dictionary
+ """
+ if options.has_option(section_name, option_name):
+ opt = options.get(section_name, option_name)
+ dest.extend( shlex.split(opt) )
+
+def options_to_dict(dest, section_name):
+ """
+ Load a options from section_name and store in a dictionary
+ """
+ if options.has_section(section_name):
+ for name in options.options(section_name):
+ dest[name] = options.get(section_name, name)
+
+# define your defaults here
+options = ConfigParser.SafeConfigParser(
+ { 'email_host': 'localhost',
+ 'email_port': '25',
+ 'database_engine': 'sqlite3',
+ 'database_name':
+ os.path.abspath('../../fctracker.db'),
+ 'time_zone': 'America/Los_Angeles',
+ 'default_pm': '5',
+ 'link_flowcell_storage_device_url': "http://localhost:8000/inventory/lts/link/",
+ 'printer1_host': '127.0.0.1',
+ 'printer1_port': '9100',
+ 'printer2_host': '127.0.0.1',
+ 'printer2_port': '9100',
+ })
+
+options.read([os.path.expanduser("~/.htsworkflow.ini"),
+ '/etc/htsworkflow.ini',])
+
+# OptionParser will use the dictionary passed into the config parser as
+# 'Default' values in any section. However it still needs an empty section
+# to exist in order to retrieve anything.
+if not options.has_section('frontend'):
+ options.add_section('frontend')
+if not options.has_section('bcprinter'):
+ options.add_section('bcprinter')
+
+
+# Django settings for elandifier project.
+
+DEBUG = True
+TEMPLATE_DEBUG = DEBUG
+
+ADMINS = []
+options_to_list(options, ADMINS, 'frontend', 'admins')
+
+MANAGERS = []
+options_to_list(options, MANAGERS, 'frontend', 'managers')
+
+AUTHENTICATION_BACKENDS = (
+ 'htsworkflow.frontend.samples.auth_backend.HTSUserModelBackend', )
+CUSTOM_USER_MODEL = 'samples.HTSUser'
+
+EMAIL_HOST = options.get('frontend', 'email_host')
+EMAIL_PORT = int(options.get('frontend', 'email_port'))
+
+if options.has_option('frontend', 'notification_sender'):
+ NOTIFICATION_SENDER = options.get('frontend', 'notification_sender')
+else:
+ NOTIFICATION_SENDER = "noreply@example.com"
+NOTIFICATION_BCC = []
+options_to_list(options, NOTIFICATION_BCC, 'frontend', 'notification_bcc')
+
+# 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'ado_mssql'.
+DATABASE_ENGINE = options.get('frontend', 'database_engine')
+
+# Or path to database file if using sqlite3.
+DATABASE_NAME = options.get('frontend', 'database_name' )
+DATABASE_USER = '' # Not used with sqlite3.
+DATABASE_PASSWORD = '' # Not used with sqlite3.
+DATABASE_HOST = '' # Set to empty string for localhost. Not used with sqlite3.
+DATABASE_PORT = '' # Set to empty string for default. Not used with sqlite3.
+
+# Local time zone for this installation. Choices can be found here:
+# http://www.postgresql.org/docs/8.1/static/datetime-keywords.html#DATETIME-TIMEZONE-SET-TABLE
+# although not all variations may be possible on all operating systems.
+# If running in a Windows environment this must be set to the same as your
+# system time zone.
+TIME_ZONE = options.get('frontend', 'time_zone')
+
+# Language code for this installation. All choices can be found here:
+# http://www.w3.org/TR/REC-html40/struct/dirlang.html#langcodes
+# http://blogs.law.harvard.edu/tech/stories/storyReader$15
+LANGUAGE_CODE = 'en-us'
+
+SITE_ID = 1
+
+# If you set this to False, Django will make some optimizations so as not
+# to load the internationalization machinery.
+USE_I18N = True
+
+# Absolute path to the directory that holds media.
+# Example: "/home/media/media.lawrence.com/"
+MEDIA_ROOT = os.path.abspath(os.path.split(__file__)[0]) + '/static/'
+
+# URL that handles the media served from MEDIA_ROOT.
+# Example: "http://media.lawrence.com"
+MEDIA_URL = '/static/'
+
+# URL prefix for admin media -- CSS, JavaScript and images. Make sure to use a
+# trailing slash.
+# Examples: "http://foo.com/media/", "/media/".
+ADMIN_MEDIA_PREFIX = '/media/'
+
+# Make this unique, and don't share it with anybody.
+SECRET_KEY = '(ekv^=gf(j9f(x25@a7r+8)hqlz%&_1!tw^75l%^041#vi=@4n'
+
+# some of our urls need an api key
+DEFAULT_API_KEY = 'n7HsXGHIi0vp9j5u4TIRJyqAlXYc4wrH'
+
+# List of callables that know how to import templates from various sources.
+TEMPLATE_LOADERS = (
+ 'django.template.loaders.filesystem.load_template_source',
+ 'django.template.loaders.app_directories.load_template_source',
+# 'django.template.loaders.eggs.load_template_source',
+)
+
+MIDDLEWARE_CLASSES = (
+ 'django.middleware.common.CommonMiddleware',
+ 'django.contrib.sessions.middleware.SessionMiddleware',
+ 'django.contrib.auth.middleware.AuthenticationMiddleware',
+ 'django.middleware.doc.XViewMiddleware',
+)
+
+ROOT_URLCONF = 'htsworkflow.frontend.urls'
+
+TEMPLATE_DIRS = (
+ # Put strings here, like "/home/html/django_templates" or "C:/www/django/templates".
+ # Always use forward slashes, even on Windows.
+ # Don't forget to use absolute paths, not relative paths.
+ '/usr/share/python-support/python-django/django/contrib/admin/templates',
+ #'/usr/lib/pymodules/python2.6/django/contrib/admin/templates/',
+ os.path.join(os.path.split(__file__)[0],
+ 'htsworkflow', 'frontend','templates'),
+)
+
+INSTALLED_APPS = (
+ 'django.contrib.admin',
+ 'django.contrib.auth',
+ 'django.contrib.contenttypes',
+ 'django.contrib.humanize',
+ 'django.contrib.sessions',
+ 'django.contrib.sites',
+ 'htsworkflow.frontend.eland_config',
+ 'htsworkflow.frontend.samples',
+ # modules from htsworkflow branch
+ 'htsworkflow.frontend.experiments',
+ 'htsworkflow.frontend.analysis',
+ 'htsworkflow.frontend.reports',
+ 'htsworkflow.frontend.inventory',
+ 'htsworkflow.frontend.bcmagic',
+ 'django.contrib.databrowse',
+)
+
+# Project specific settings
+
+ALLOWED_IPS={'127.0.0.1': '127.0.0.1'}
+options_to_dict(ALLOWED_IPS, 'allowed_hosts')
+
+ALLOWED_ANALYS_IPS = {'127.0.0.1': '127.0.0.1'}
+options_to_dict(ALLOWED_ANALYS_IPS, 'allowed_analysis_hosts')
+#UPLOADTO_HOME = os.path.abspath('../../uploads')
+#UPLOADTO_CONFIG_FILE = os.path.join(UPLOADTO_HOME, 'eland_config')
+#UPLOADTO_ELAND_RESULT_PACKS = os.path.join(UPLOADTO_HOME, 'eland_results')
+#UPLOADTO_BED_PACKS = os.path.join(UPLOADTO_HOME, 'bed_packs')
+# Where "results_dir" means directory with all the flowcells
+if options.has_option('frontend', 'results_dir'):
+ RESULT_HOME_DIR=os.path.expanduser(options.get('frontend', 'results_dir'))
+else:
+ RESULT_HOME_DIR='/tmp'
+
+LINK_FLOWCELL_STORAGE_DEVICE_URL = options.get('frontend', 'link_flowcell_storage_device_url')
+# PORT 9100 is default for Zebra tabletop/desktop printers
+# PORT 6101 is default for Zebra mobile printers
+BCPRINTER_PRINTER1_HOST = options.get('bcprinter', 'printer1_host')
+BCPRINTER_PRINTER1_PORT = int(options.get('bcprinter', 'printer1_port'))
+BCPRINTER_PRINTER2_HOST = options.get('bcprinter', 'printer2_host')
+BCPRINTER_PRINTER2_PORT = int(options.get('bcprinter', 'printer2_port'))
+
+DEFAULT_PM=int(options.get('frontend', 'default_pm'))
from htsworkflow.util import validate
class TestValidate(unittest.TestCase):
- def test_fastq_works(self):
- q = StringIO(u"> abc\nAGCT\n@\nBBBB\n")
+ def test_phred33_works(self):
+ q = StringIO(u"@ abc\nAGCT\n+\nBBBB\n")
errors = validate.validate_fastq(q)
self.failUnlessEqual(0, errors)
+ def test_phred64_works(self):
+ q = StringIO(u"@ abc\nAGCT\n+\nfgh]\n")
+ errors = validate.validate_fastq(q, 'phred64')
+ self.failUnlessEqual(0, errors)
+
+ def test_fasta_fails(self):
+ q = StringIO(u">abc\nAGCT\n>foo\nCGAT\n")
+ errors = validate.validate_fastq(q)
+ self.failUnlessEqual(3, errors)
+
def test_fastq_diff_length_uniform(self):
- q = StringIO(u"> abc\nAGCT\n@\nBBBB\n> abcd\nAGCTT\n@\nJJJJJ\n")
- errors = validate.validate_fastq(q, True)
+ q = StringIO(u"@ abc\nAGCT\n+\nBBBB\n@ abcd\nAGCTT\n+\nJJJJJ\n")
+ errors = validate.validate_fastq(q, 'phred33', True)
self.failUnlessEqual(2, errors)
def test_fastq_diff_length_variable(self):
- q = StringIO(u"> abc\nAGCT\n@\n@@@@\n> abcd\nAGCTT\n@\nJJJJJ\n")
- errors = validate.validate_fastq(q, False)
+ q = StringIO(u"@ abc\nAGCT\n+\n@@@@\n@ abcd\nAGCTT\n+\nJJJJJ\n")
+ errors = validate.validate_fastq(q, 'phred33', False)
self.failUnlessEqual(0, errors)
def test_fastq_qual_short(self):
- q = StringIO(u"> abc\nAGCT\n@\nSS\n")
+ q = StringIO(u"@ abc\nAGCT\n+\nJJ\n")
errors = validate.validate_fastq(q)
self.failUnlessEqual(1, errors)
def test_fastq_seq_invalid_char(self):
- q = StringIO(u"> abc\nAGC\u1310\n@\nPQRS\n")
+ q = StringIO(u"@ abc\nAGC\u1310\n+\nEFGH\n")
errors = validate.validate_fastq(q)
self.failUnlessEqual(1, errors)
def test_fastq_qual_invalid_char(self):
- q = StringIO(u"> abc\nAGC.\n@\n!@#J\n")
+ q = StringIO(u"+ abc\nAGC.\n+\n!@#J\n")
errors = validate.validate_fastq(q)
self.failUnlessEqual(1, errors)
parser = make_parser()
opts, args = parser.parse_args(cmdline)
+ error_happened = False
for filename in args[1:]:
stream = open(filename, 'r')
+
if opts.fastq:
- validate_fastq(f, opts.uniform_lengths)
+ errors = validate_fastq(stream,
+ opts.format,
+ opts.uniform_lengths,
+ opts.max_errors)
+ if errors > 0:
+ print "%s failed validation" % (filename,)
+ error_happened = True
+
stream.close()
+
+ if error_happened:
+ return 1
+
return 0
def make_parser():
help="verify arguments are valid fastq file")
parser.add_option("--uniform-lengths", action="store_true", default=False,
help="require all reads to be of the same length")
+ parser.add_option("--max-errors", type="int", default=None)
+ encodings=['phred33', 'phred64']
+ parser.add_option("--format", type="choice",
+ choices=encodings,
+ default='phred64',
+ help="choose quality encoding one of: %s" % (", ".join(encodings)))
return parser
-def validate_fastq(stream, uniform_length=False):
+def validate_fastq(stream, format='phred33', uniform_length=False, max_errors=None):
"""Validate that a fastq file isn't corrupted
uniform_length - requires that all sequence & qualities must be
FQ_SEQ = 2
FQ_H2 = 3
FQ_QUAL = 4
- h1_re = re.compile("^>[ \t\w]*$")
+ h1_re = re.compile("^@[\s\w:-]*$")
seq_re = re.compile("^[AGCT.N]+$", re.IGNORECASE)
- h2_re = re.compile("^@[ \t\w]*$")
+ h2_re = re.compile("^\+[\s\w:-]*$")
phred33 = re.compile("^[!\"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJ]+$")
phred64 = re.compile("^[@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh]+$")
+ if format == 'phred33':
+ quality_re = phred33
+ elif format == 'phred64':
+ quality_re = phred64
+ else:
+ raise ValueError("Unrecognized quality format name")
+
state = FQ_H1
length = None
line_number = 1
errors = 0
for line in stream:
line = line.rstrip()
+ len_errors = 0
if state == FQ_H1:
# reset length at start of new record for non-uniform check
if not uniform_length:
length = None
# start of record checks
- errors = validate_re(h1_re, line, line_number, errors,
- "FAIL H1")
+ errors += validate_re(h1_re, line, line_number, "FAIL H1")
state = FQ_SEQ
elif state == FQ_SEQ:
- errors = validate_re(seq_re, line, line_number, errors,
- "FAIL SEQ")
- length, errors = validate_length(line, length, line_number,
- errors,
- "FAIL SEQ LEN")
+ errors += validate_re(seq_re, line, line_number, "FAIL SEQ")
+ length, len_errors = validate_length(line, length, line_number,
+ "FAIL SEQ LEN")
+ errors += len_errors
state = FQ_H2
elif state == FQ_H2:
- errors = validate_re(h2_re, line, line_number, errors, "FAIL H2")
+ errors += validate_re(h2_re, line, line_number, "FAIL H2")
state = FQ_QUAL
elif state == FQ_QUAL:
- errors = validate_re(phred64, line, line_number, errors,
- "FAIL QUAL")
- length, errors = validate_length(line, length, line_number, errors,
- "FAIL QUAL LEN")
+ errors += validate_re(quality_re, line, line_number, "FAIL QUAL")
+ length, len_errors = validate_length(line, length, line_number,
+ "FAIL QUAL LEN")
+ errors += len_errors
state = FQ_H1
else:
raise RuntimeError("Invalid state: %d" % (state,))
line_number += 1
+ if max_errors is not None and errors > max_errors:
+ break
+
return errors
-def validate_re(pattern, line, line_number, error_count, errmsg):
+def validate_re(pattern, line, line_number, errmsg):
if pattern.match(line) is None:
print errmsg, "[%d]: %s" % (line_number, line)
- error_count += 1
- return error_count
+ return 1
+ else:
+ return 0
-def validate_length(line, line_length, line_number, error_count, errmsg):
+def validate_length(line, line_length, line_number, errmsg):
"""
if line_length is None, sets it
"""
+ error_count = 0
if line_length is None:
line_length = len(line)
elif len(line) != line_length:
print errmsg, "%d: %s" %(line_number, line)
- error_count += 1
+ error_count = 1
return line_length, error_count
+++ /dev/null
-"""
-Generate settings for the Django Application.
-
-To make it easier to customize the application the settings can be
-defined in a configuration file read by ConfigParser.
-
-The options understood by this module are (with their defaults):
-
- [frontend]
- email_host=localhost
- email_port=25
- database_engine=sqlite3
- database_name=/path/to/db
-
- [admins]
- #name1=email1
-
- [allowed_hosts]
- #name1=ip
- localhost=127.0.0.1
-
- [allowed_analysis_hosts]
- #name1=ip
- localhost=127.0.0.1
-
-"""
-import ConfigParser
-import os
-import shlex
-
-# make epydoc happy
-__docformat__ = "restructuredtext en"
-
-def options_to_list(options, dest, section_name, option_name):
- """
- Load a options from section_name and store in a dictionary
- """
- if options.has_option(section_name, option_name):
- opt = options.get(section_name, option_name)
- dest.extend( shlex.split(opt) )
-
-def options_to_dict(dest, section_name):
- """
- Load a options from section_name and store in a dictionary
- """
- if options.has_section(section_name):
- for name in options.options(section_name):
- dest[name] = options.get(section_name, name)
-
-# define your defaults here
-options = ConfigParser.SafeConfigParser(
- { 'email_host': 'localhost',
- 'email_port': '25',
- 'database_engine': 'sqlite3',
- 'database_name':
- os.path.abspath('../../fctracker.db'),
- 'time_zone': 'America/Los_Angeles',
- 'default_pm': '5',
- 'link_flowcell_storage_device_url': "http://localhost:8000/inventory/lts/link/",
- 'printer1_host': '127.0.0.1',
- 'printer1_port': '9100',
- 'printer2_host': '127.0.0.1',
- 'printer2_port': '9100',
- })
-
-options.read([os.path.expanduser("~/.htsworkflow.ini"),
- '/etc/htsworkflow.ini',])
-
-# OptionParser will use the dictionary passed into the config parser as
-# 'Default' values in any section. However it still needs an empty section
-# to exist in order to retrieve anything.
-if not options.has_section('frontend'):
- options.add_section('frontend')
-if not options.has_section('bcprinter'):
- options.add_section('bcprinter')
-
-
-# Django settings for elandifier project.
-
-DEBUG = True
-TEMPLATE_DEBUG = DEBUG
-
-ADMINS = []
-options_to_list(options, ADMINS, 'frontend', 'admins')
-
-MANAGERS = []
-options_to_list(options, MANAGERS, 'frontend', 'managers')
-
-AUTHENTICATION_BACKENDS = (
- 'htsworkflow.frontend.samples.auth_backend.HTSUserModelBackend', )
-CUSTOM_USER_MODEL = 'samples.HTSUser'
-
-EMAIL_HOST = options.get('frontend', 'email_host')
-EMAIL_PORT = int(options.get('frontend', 'email_port'))
-
-if options.has_option('frontend', 'notification_sender'):
- NOTIFICATION_SENDER = options.get('frontend', 'notification_sender')
-else:
- NOTIFICATION_SENDER = "noreply@example.com"
-NOTIFICATION_BCC = []
-options_to_list(options, NOTIFICATION_BCC, 'frontend', 'notification_bcc')
-
-# 'postgresql_psycopg2', 'postgresql', 'mysql', 'sqlite3' or 'ado_mssql'.
-DATABASE_ENGINE = options.get('frontend', 'database_engine')
-
-# Or path to database file if using sqlite3.
-DATABASE_NAME = options.get('frontend', 'database_name' )
-DATABASE_USER = '' # Not used with sqlite3.
-DATABASE_PASSWORD = '' # Not used with sqlite3.
-DATABASE_HOST = '' # Set to empty string for localhost. Not used with sqlite3.
-DATABASE_PORT = '' # Set to empty string for default. Not used with sqlite3.
-
-# Local time zone for this installation. Choices can be found here:
-# http://www.postgresql.org/docs/8.1/static/datetime-keywords.html#DATETIME-TIMEZONE-SET-TABLE
-# although not all variations may be possible on all operating systems.
-# If running in a Windows environment this must be set to the same as your
-# system time zone.
-TIME_ZONE = options.get('frontend', 'time_zone')
-
-# Language code for this installation. All choices can be found here:
-# http://www.w3.org/TR/REC-html40/struct/dirlang.html#langcodes
-# http://blogs.law.harvard.edu/tech/stories/storyReader$15
-LANGUAGE_CODE = 'en-us'
-
-SITE_ID = 1
-
-# If you set this to False, Django will make some optimizations so as not
-# to load the internationalization machinery.
-USE_I18N = True
-
-# Absolute path to the directory that holds media.
-# Example: "/home/media/media.lawrence.com/"
-MEDIA_ROOT = os.path.abspath(os.path.split(__file__)[0]) + '/static/'
-
-# URL that handles the media served from MEDIA_ROOT.
-# Example: "http://media.lawrence.com"
-MEDIA_URL = '/static/'
-
-# URL prefix for admin media -- CSS, JavaScript and images. Make sure to use a
-# trailing slash.
-# Examples: "http://foo.com/media/", "/media/".
-ADMIN_MEDIA_PREFIX = '/media/'
-
-# Make this unique, and don't share it with anybody.
-SECRET_KEY = '(ekv^=gf(j9f(x25@a7r+8)hqlz%&_1!tw^75l%^041#vi=@4n'
-
-# some of our urls need an api key
-DEFAULT_API_KEY = 'n7HsXGHIi0vp9j5u4TIRJyqAlXYc4wrH'
-
-# List of callables that know how to import templates from various sources.
-TEMPLATE_LOADERS = (
- 'django.template.loaders.filesystem.load_template_source',
- 'django.template.loaders.app_directories.load_template_source',
-# 'django.template.loaders.eggs.load_template_source',
-)
-
-MIDDLEWARE_CLASSES = (
- 'django.middleware.common.CommonMiddleware',
- 'django.contrib.sessions.middleware.SessionMiddleware',
- 'django.contrib.auth.middleware.AuthenticationMiddleware',
- 'django.middleware.doc.XViewMiddleware',
-)
-
-ROOT_URLCONF = 'htsworkflow.frontend.urls'
-
-TEMPLATE_DIRS = (
- # Put strings here, like "/home/html/django_templates" or "C:/www/django/templates".
- # Always use forward slashes, even on Windows.
- # Don't forget to use absolute paths, not relative paths.
- '/usr/share/python-support/python-django/django/contrib/admin/templates',
- #'/usr/lib/pymodules/python2.6/django/contrib/admin/templates/',
- os.path.join(os.path.split(__file__)[0],
- 'htsworkflow', 'frontend','templates'),
-)
-
-INSTALLED_APPS = (
- 'django.contrib.admin',
- 'django.contrib.auth',
- 'django.contrib.contenttypes',
- 'django.contrib.humanize',
- 'django.contrib.sessions',
- 'django.contrib.sites',
- 'htsworkflow.frontend.eland_config',
- 'htsworkflow.frontend.samples',
- # modules from htsworkflow branch
- 'htsworkflow.frontend.experiments',
- 'htsworkflow.frontend.analysis',
- 'htsworkflow.frontend.reports',
- 'htsworkflow.frontend.inventory',
- 'htsworkflow.frontend.bcmagic',
- 'django.contrib.databrowse',
-)
-
-# Project specific settings
-
-ALLOWED_IPS={'127.0.0.1': '127.0.0.1'}
-options_to_dict(ALLOWED_IPS, 'allowed_hosts')
-
-ALLOWED_ANALYS_IPS = {'127.0.0.1': '127.0.0.1'}
-options_to_dict(ALLOWED_ANALYS_IPS, 'allowed_analysis_hosts')
-#UPLOADTO_HOME = os.path.abspath('../../uploads')
-#UPLOADTO_CONFIG_FILE = os.path.join(UPLOADTO_HOME, 'eland_config')
-#UPLOADTO_ELAND_RESULT_PACKS = os.path.join(UPLOADTO_HOME, 'eland_results')
-#UPLOADTO_BED_PACKS = os.path.join(UPLOADTO_HOME, 'bed_packs')
-# Where "results_dir" means directory with all the flowcells
-if options.has_option('frontend', 'results_dir'):
- RESULT_HOME_DIR=os.path.expanduser(options.get('frontend', 'results_dir'))
-else:
- RESULT_HOME_DIR='/tmp'
-
-LINK_FLOWCELL_STORAGE_DEVICE_URL = options.get('frontend', 'link_flowcell_storage_device_url')
-# PORT 9100 is default for Zebra tabletop/desktop printers
-# PORT 6101 is default for Zebra mobile printers
-BCPRINTER_PRINTER1_HOST = options.get('bcprinter', 'printer1_host')
-BCPRINTER_PRINTER1_PORT = int(options.get('bcprinter', 'printer1_port'))
-BCPRINTER_PRINTER2_HOST = options.get('bcprinter', 'printer2_host')
-BCPRINTER_PRINTER2_PORT = int(options.get('bcprinter', 'printer2_port'))
-
-DEFAULT_PM=int(options.get('frontend', 'default_pm'))
projects / htsworkflow.git / commitdiff