+++ /dev/null
-#!/usr/bin/python
-import subprocess
-import logging
-import time
-import re
-import os
-
-from retrieve_eland_config import getCombinedOptions, saveConfigFile
-from retrieve_eland_config import FlowCellNotFound, WebError404
-from genome_mapper import DuplicateGenome, getAvailableGenomes, constructMapperDict
-
-from pyinotify import WatchManager, ThreadedNotifier
-from pyinotify import EventsCodes, ProcessEvent
-
-logging.basicConfig(level=logging.DEBUG,
- format='%(asctime)s %(levelname)-8s %(message)s',
- datefmt='%a, %d %b %Y %H:%M:%S',
- filename='pipeline_main.log',
- filemode='w')
-
-class ConfigInfo:
-
- def __init__(self):
- self.run_path = None
- self.bustard_path = None
- self.config_filepath = None
-
-
-####################################
-# inotify event processor
-
-s_firecrest_finished = re.compile('Firecrest[0-9\._\-A-Za-z]+/finished.txt')
-s_bustard_finished = re.compile('Bustard[0-9\._\-A-Za-z]+/finished.txt')
-s_gerald_finished = re.compile('GERALD[0-9\._\-A-Za-z]+/finished.txt')
-
-class RunEvent(ProcessEvent):
-
- def __init__(self):
-
- self.run_status_dict = {'firecrest': False,
- 'bustard': False,
- 'gerald': False}
-
- ProcessEvent.__init__(self)
-
- def process_IN_CREATE(self, event):
- fullpath = os.path.join(event.path, event.name)
- if s_finished.search(fullpath):
- logging.info("File Found: %s" % (fullpath))
-
- if s_firecrest_finished.search(fullpath):
- self.run_status_dict['firecrest'] = True
- elif s_bustard_finished.search(fullpath):
- self.run_status_dict['bustard'] = True
- elif s_gerald_finished.search(fullpath):
- self.run_status_dict['gerald'] = True
-
- print "Create: %s" % (os.path.join(event.path, event.name))
-
- def process_IN_DELETE(self, event):
- print "Remove %s" % (os.path.join(event.path, event.name))
-
-#FLAGS
-# Config Step Error
-RUN_ABORT = 'abort'
-# Run Step Error
-RUN_FAILED = 'failed'
-
-
-#####################################
-# Configure Step (goat_pipeline.py)
-#Info
-s_start = re.compile('Starting Genome Analyzer Pipeline')
-s_gerald = re.compile("[\S\s]+--GERALD[\S\s]+--make[\S\s]+")
-s_generating = re.compile('Generating journals, Makefiles and parameter files')
-s_seq_folder = re.compile('^Sequence folder: ')
-s_seq_folder_sub = re.compile('want to make ')
-s_stderr_taskcomplete = re.compile('^Task complete, exiting')
-
-#Errors
-s_invalid_cmdline = re.compile('Usage:[\S\s]*goat_pipeline.py')
-s_species_dir_err = re.compile('Error: Lane [1-8]:')
-s_goat_traceb = re.compile("^Traceback \(most recent call last\):")
-
-
-##Ignore - Example of out above each ignore regex.
-#NOTE: Commenting out an ignore will cause it to be
-# logged as DEBUG with the logging module.
-#CF_STDERR_IGNORE_LIST = []
-s_skip = re.compile('s_[0-8]_[0-9]+')
-
-
-##########################################
-# Pipeline Run Step (make -j8 recursive)
-
-##Info
-s_finished = re.compile('finished')
-
-##Errors
-s_make_error = re.compile('^make[\S\s]+Error')
-s_no_gnuplot = re.compile('gnuplot: command not found')
-s_no_convert = re.compile('^Can\'t exec "convert"')
-s_no_ghostscript = re.compile('gs: command not found')
-
-##Ignore - Example of out above each ignore regex.
-#NOTE: Commenting out an ignore will cause it to be
-# logged as DEBUG with the logging module.
-#
-PL_STDERR_IGNORE_LIST = []
-# Info: PF 11802
-PL_STDERR_IGNORE_LIST.append( re.compile('^Info: PF') )
-# About to analyse intensity file s_4_0101_sig2.txt
-PL_STDERR_IGNORE_LIST.append( re.compile('^About to analyse intensity file') )
-# Will send output to standard output
-PL_STDERR_IGNORE_LIST.append( re.compile('^Will send output to standard output') )
-# Found 31877 clusters
-PL_STDERR_IGNORE_LIST.append( re.compile('^Found [0-9]+ clusters') )
-# Will use quality criterion ((CHASTITY>=0.6)
-PL_STDERR_IGNORE_LIST.append( re.compile('^Will use quality criterion') )
-# Quality criterion translated to (($F[5]>=0.6))
-PL_STDERR_IGNORE_LIST.append( re.compile('^Quality criterion translated to') )
-# opened /woldlab/trog/data1/king/070924_USI-EAS44_0022_FC12150/Data/C1-36_Firecrest1.9.1_14-11-2007_king.4/Bustard1.9.1_14-11-2007_king/s_4_0101_qhg.txt
-# AND
-# opened s_4_0103_qhg.txt
-PL_STDERR_IGNORE_LIST.append( re.compile('^opened[\S\s]+qhg.txt') )
-# 81129 sequences out of 157651 passed filter criteria
-PL_STDERR_IGNORE_LIST.append( re.compile('^[0-9]+ sequences out of [0-9]+ passed filter criteria') )
-
-
-def pl_stderr_ignore(line):
- """
- Searches lines for lines to ignore (i.e. not to log)
-
- returns True if line should be ignored
- returns False if line should NOT be ignored
- """
- for s in PL_STDERR_IGNORE_LIST:
- if s.search(line):
- return True
- return False
-
-
-def config_stdout_handler(line, conf_info):
- """
- Processes each line of output from GOAT
- and stores useful information using the logging module
-
- Loads useful information into conf_info as well, for future
- use outside the function.
-
- returns True if found condition that signifies success.
- """
-
- # Skip irrelevant line (without logging)
- if s_skip.search(line):
- pass
-
- # Detect invalid command-line arguments
- elif s_invalid_cmdline.search(line):
- logging.error("Invalid commandline options!")
-
- # Detect starting of configuration
- elif s_start.search(line):
- logging.info('START: Configuring pipeline')
-
- # Detect it made it past invalid arguments
- elif s_gerald.search(line):
- logging.info('Running make now')
-
- # Detect that make files have been generated (based on output)
- elif s_generating.search(line):
- logging.info('Make files generted')
- return True
-
- # Capture run directory
- elif s_seq_folder.search(line):
- mo = s_seq_folder_sub.search(line)
- #Output changed when using --tiles=<tiles>
- # at least in pipeline v0.3.0b2
- if mo:
- firecrest_bustard_gerald_makefile = line[mo.end():]
- firecrest_bustard_gerald, junk = \
- os.path.split(firecrest_bustard_gerald_makefile)
- firecrest_bustard, junk = os.path.split(firecrest_bustard_gerald)
- firecrest, junk = os.path.split(firecrest_bustard)
-
- conf_info.bustard_path = firecrest_bustard
- conf_info.run_path = firecrest
-
- #Standard output handling
- else:
- print 'Sequence line:', line
- mo = s_seq_folder.search(line)
- conf_info.bustard_path = line[mo.end():]
- conf_info.run_path, temp = os.path.split(conf_info.bustard_path)
-
- # Log all other output for debugging purposes
- else:
- logging.warning('CONF:?: %s' % (line))
-
- return False
-
-
-
-def config_stderr_handler(line, conf_info):
- """
- Processes each line of output from GOAT
- and stores useful information using the logging module
-
- Loads useful information into conf_info as well, for future
- use outside the function.
-
- returns RUN_ABORT upon detecting failure;
- True on success message;
- False if neutral message
- (i.e. doesn't signify failure or success)
- """
-
- # Detect invalid species directory error
- if s_species_dir_err.search(line):
- logging.error(line)
- return RUN_ABORT
- # Detect goat_pipeline.py traceback
- elif s_goat_traceb.search(line):
- logging.error("Goat config script died, traceback in debug output")
- return RUN_ABORT
- # Detect indication of successful configuration (from stderr; odd, but ok)
- elif s_stderr_taskcomplete.search(line):
- logging.info('Configure step successful (from: stderr)')
- return True
- # Log all other output as debug output
- else:
- logging.debug('CONF:STDERR:?: %s' % (line))
-
- # Neutral (not failure; nor success)
- return False
-
-
-#def pipeline_stdout_handler(line, conf_info):
-# """
-# Processes each line of output from running the pipeline
-# and stores useful information using the logging module
-#
-# Loads useful information into conf_info as well, for future
-# use outside the function.
-#
-# returns True if found condition that signifies success.
-# """
-#
-# #f.write(line + '\n')
-#
-# return True
-
-
-
-def pipeline_stderr_handler(line, conf_info):
- """
- Processes each line of stderr from pipelien run
- and stores useful information using the logging module
-
- ##FIXME: Future feature (doesn't actually do this yet)
- #Loads useful information into conf_info as well, for future
- #use outside the function.
-
- returns RUN_FAILED upon detecting failure;
- #True on success message; (no clear success state)
- False if neutral message
- (i.e. doesn't signify failure or success)
- """
-
- if pl_stderr_ignore(line):
- pass
- elif s_make_error.search(line):
- logging.error("make error detected; run failed")
- return RUN_FAILED
- elif s_no_gnuplot.search(line):
- logging.error("gnuplot not found")
- return RUN_FAILED
- elif s_no_convert.search(line):
- logging.error("imagemagick's convert command not found")
- return RUN_FAILED
- elif s_no_ghostscript.search(line):
- logging.error("ghostscript not found")
- return RUN_FAILED
- else:
- logging.debug('PIPE:STDERR:?: %s' % (line))
-
- return False
-
-
-def retrieve_config(conf_info, flowcell, cfg_filepath, genome_dir):
- """
- Gets the config file from server...
- requires config file in:
- /etc/ga_frontend/ga_frontend.conf
- or
- ~/.ga_frontend.conf
-
- with:
- [config_file_server]
- base_host_url: http://host:port
-
- return True if successful, False is failure
- """
- options = getCombinedOptions()
-
- if options.url is None:
- logging.error("~/.ga_frontend.conf or /etc/ga_frontend/ga_frontend.conf" \
- " missing base_host_url option")
- return False
-
- try:
- saveConfigFile(flowcell, options.url, cfg_filepath)
- conf_info.config_filepath = cfg_filepath
- except FlowCellNotFound, e:
- logging.error(e)
- return False
- except WebError404, e:
- logging.error(e)
- return False
- except IOError, e:
- logging.error(e)
- return False
- except Exception, e:
- logging.error(e)
- return False
-
- f = open(cfg_filepath, 'r')
- data = f.read()
- f.close()
-
- genome_dict = getAvailableGenomes(genome_dir)
- mapper_dict = constructMapperDict(genome_dict)
-
- f = open(cfg_filepath, 'w')
- f.write(data % (mapper_dict))
- f.close()
-
- return True
-
-
-
-def configure(conf_info):
- """
- Attempts to configure the GA pipeline using goat.
-
- Uses logging module to store information about status.
-
- returns True if configuration successful, otherwise False.
- """
- #ERROR Test:
- #pipe = subprocess.Popen(['goat_pipeline.py',
- # '--GERALD=config32bk.txt',
- # '--make .',],
- # #'.'],
- # stdout=subprocess.PIPE,
- # stderr=subprocess.PIPE)
-
- #ERROR Test (2), causes goat_pipeline.py traceback
- #pipe = subprocess.Popen(['goat_pipeline.py',
- # '--GERALD=%s' % (conf_info.config_filepath),
- # '--tiles=s_4_100,s_4_101,s_4_102,s_4_103,s_4_104',
- # '--make',
- # '.'],
- # stdout=subprocess.PIPE,
- # stderr=subprocess.PIPE)
-
- ##########################
- # Run configuration step
- # Not a test; actual configure attempt.
- #pipe = subprocess.Popen(['goat_pipeline.py',
- # '--GERALD=%s' % (conf_info.config_filepath),
- # '--make',
- # '.'],
- # stdout=subprocess.PIPE,
- # stderr=subprocess.PIPE)
-
- # CONTINUE HERE
- #FIXME: this only does a run on 5 tiles on lane 4
- pipe = subprocess.Popen(['goat_pipeline.py',
- '--GERALD=%s' % (conf_info.config_filepath),
- '--tiles=s_4_0100,s_4_0101,s_4_0102,s_4_0103,s_4_0104',
- '--make',
- '.'],
- stdout=subprocess.PIPE,
- stderr=subprocess.PIPE)
- ##################
- # Process stdout
- stdout_line = pipe.stdout.readline()
-
- complete = False
- while stdout_line != '':
- # Handle stdout
- if config_stdout_handler(stdout_line, conf_info):
- complete = True
- stdout_line = pipe.stdout.readline()
-
-
- error_code = pipe.wait()
- if error_code:
- logging.error('Recieved error_code: %s' % (error_code))
- else:
- logging.info('We are go for launch!')
-
- #Process stderr
- stderr_line = pipe.stderr.readline()
-
- abort = 'NO!'
- stderr_success = False
- while stderr_line != '':
- stderr_status = config_stderr_handler(stderr_line, conf_info)
- if stderr_status == RUN_ABORT:
- abort = RUN_ABORT
- elif stderr_status is True:
- stderr_success = True
- stderr_line = pipe.stderr.readline()
-
-
- #Success requirements:
- # 1) The stdout completed without error
- # 2) The program exited with status 0
- # 3) No errors found in stdout
- print '#Expect: True, False, True, True'
- print complete, bool(error_code), abort != RUN_ABORT, stderr_success is True
- status = complete is True and \
- bool(error_code) is False and \
- abort != RUN_ABORT and \
- stderr_success is True
-
- # If everything was successful, but for some reason
- # we didn't retrieve the path info, log it.
- if status is True:
- if conf_info.bustard_path is None or conf_info.run_path is None:
- logging.error("Failed to retrieve run_path")
- return False
-
- return status
-
-
-def run_pipeline(conf_info):
- """
- Run the pipeline and monitor status.
- """
- # Fail if the run_path doesn't actually exist
- if not os.path.exists(conf_info.run_path):
- logging.error('Run path does not exist: %s' \
- % (conf_info.run_path))
- return False
-
- # Change cwd to run_path
- os.chdir(conf_info.run_path)
- stdout_filepath = os.path.join(conf_info.run_path, 'pipeline_run_stdout.txt')
- stderr_filepath = os.path.join(conf_info.run_path, 'pipeline_run_stderr.txt')
-
- # Monitor file creation
- wm = WatchManager()
- mask = EventsCodes.IN_DELETE | EventsCodes.IN_CREATE
- event = RunEvent()
- notifier = ThreadedNotifier(wm, event)
- notifier.start()
- wdd = wm.add_watch(conf_info.run_path, mask, rec=True)
-
- # Log pipeline starting
- logging.info('STARTING PIPELINE @ %s' % (time.ctime()))
-
- # Start the pipeline (and hide!)
- #pipe = subprocess.Popen(['make',
- # '-j8',
- # 'recursive'],
- # stdout=subprocess.PIPE,
- # stderr=subprocess.PIPE)
-
- fout = open(stdout_filepath, 'w')
- ferr = open(stderr_filepath, 'w')
-
- pipe = subprocess.Popen(['make',
- '-j8',
- 'recursive'],
- stdout=fout,
- stderr=ferr)
- #shell=True)
- # Wait for run to finish
- retcode = pipe.wait()
-
-
- # Clean up
- notifier.stop()
- fout.close()
- ferr.close()
-
- # Process stderr
- ferr = open(stderr_filepath, 'r')
-
- run_failed_stderr = False
- for line in ferr:
- err_status = pipeline_stderr_handler(line, conf_info)
- if err_status == RUN_FAILED:
- run_failed_stderr = True
-
- ferr.close()
-
- # Finished file check!
- print 'RUN SUCCESS CHECK:'
- for key, value in event.run_status_dict.items():
- print ' %s: %s' % (key, value)
-
- dstatus = event.run_status_dict
-
- # Success or failure check
- status = (retcode == 0) and \
- run_failed_stderr is False and \
- dstatus['firecrest'] is True and \
- dstatus['bustard'] is True and \
- dstatus['gerald'] is True
-
- return status
-
-
-
-if __name__ == '__main__':
- ci = ConfigInfo()
-
- flowcell = 'FC12150'
- cfg_filepath = 'config32auto.txt'
- genome_dir = '/home/king/trog_drive/'
-
- status_retrieve_cfg = retrieve_config(ci, flowcell, cfg_filepath, genome_dir)
- if status_retrieve_cfg:
- print "Retrieve config file successful"
- else:
- print "Failed to retrieve config file"
- #ci.config_filepath = 'config32bk.txt'
-
- if status_retrieve_cfg:
- status = configure(ci)
- if status:
- print "Configure success"
- else:
- print "Configure failed"
-
- print 'Run Dir:', ci.run_path
- print 'Bustard Dir:', ci.bustard_path
-
- if status:
- print 'Running pipeline now!'
- run_status = run_pipeline(ci)
- if run_status is True:
- print 'Pipeline ran successfully.'
- else:
- print 'Pipeline run failed.'
-
+++ /dev/null
-#!/usr/bin/python
-import glob
-import sys
-import os
-
-import logging
-
-class DuplicateGenome(Exception): pass
-
-
-def _has_metainfo(genome_dir):
- metapath = os.path.join(genome_dir, '_metainfo_')
- if os.path.isfile(metapath):
- return True
- else:
- return False
-
-def getAvailableGenomes(genome_base_dir):
- """
- raises IOError (on genome_base_dir not found)
- raises DuplicateGenome on duplicate genomes found.
-
- returns a double dictionary (i.e. d[species][build] = path)
- """
-
- # Need valid directory
- if not os.path.exists(genome_base_dir):
- msg = "Directory does not exist: %s" % (genome_base_dir)
- raise IOError, msg
-
- # Find all subdirectories
- filepath_list = glob.glob(os.path.join(genome_base_dir, '*'))
- potential_genome_dirs = \
- [ filepath for filepath in filepath_list if os.path.isdir(filepath)]
-
- # Get list of metadata files
- genome_dir_list = \
- [ dirpath \
- for dirpath in potential_genome_dirs \
- if _has_metainfo(dirpath) ]
-
- # Genome double dictionary
- d = {}
-
- for genome_dir in genome_dir_list:
- line = open(os.path.join(genome_dir, '_metainfo_'), 'r').readline().strip()
-
- # Get species, build... log and skip on failure
- try:
- species, build = line.split('|')
- except:
- logging.warning('Skipping: Invalid metafile (%s) line: %s' \
- % (metafile, line))
- continue
-
- build_dict = d.setdefault(species, {})
- if build in build_dict:
- msg = "Duplicate genome for %s|%s" % (species, build)
- raise DuplicateGenome, msg
-
- build_dict[build] = genome_dir
-
- return d
-
-
-def constructMapperDict(genome_dict):
- """
- Creates a dictionary which can map the genome
- in the eland config generator output to a local
- genome path
-
- ie. 'Homo sapiens|hg18' -> <genome_dir>
- """
- mapper_dict = {}
- for species in genome_dict.keys():
- for build in genome_dict[species]:
- mapper_dict[species+'|'+build] = genome_dict[species][build]
-
- return mapper_dict
-
-
-if __name__ == '__main__':
-
- if len(sys.argv) != 2:
- print 'useage: %s <base_genome_dir>' % (sys.argv[0])
- sys.exit(1)
-
- d = getAvailableGenomes(sys.argv[1])
- d2 = constructMapperDict(d)
-
- for k,v in d2.items():
- print '%s: %s' % (k,v)
-
-
+++ /dev/null
-#!/usr/bin/env python
-
-from optparse import OptionParser, IndentedHelpFormatter
-from ConfigParser import SafeConfigParser
-
-import os
-import sys
-import urllib
-
-CONFIG_SYSTEM = '/etc/ga_frontend/ga_frontend.conf'
-CONFIG_USER = os.path.expanduser('~/.ga_frontend.conf')
-
-
-class FlowCellNotFound(Exception): pass
-class WebError404(Exception): pass
-
-
-class PreformattedDescriptionFormatter(IndentedHelpFormatter):
-
- #def format_description(self, description):
- #
- # if description:
- # return description + "\n"
- # else:
- # return ""
-
- def format_epilog(self, epilog):
- """
- It was removing my preformated epilog, so this should override
- that behavior! Muhahaha!
- """
- if epilog:
- return "\n" + epilog + "\n"
- else:
- return ""
-
-
-def constructOptionParser():
- """
- returns a pre-setup optparser
- """
- parser = OptionParser(formatter=PreformattedDescriptionFormatter())
-
- parser.set_description('Retrieves eland config file from ga_frontend web frontend.')
-
- parser.epilog = """
-Config File:
- * %s (System wide)
- * %s (User specific; overrides system)
- * command line overrides all config file options
-
- Example Config File:
-
- [server_info]
- base_host_url=http://somewhere.domain:port
-""" % (CONFIG_SYSTEM, CONFIG_USER)
-
- #Special formatter for allowing preformatted description.
- ##parser.format_epilog(PreformattedDescriptionFormatter())
-
- parser.add_option("-u", "--url",
- action="store", type="string", dest="url")
-
- parser.add_option("-o", "--output",
- action="store", type="string", dest="output_filepath")
-
- parser.add_option("-f", "--flowcell",
- action="store", type="string", dest="flowcell")
-
- #parser.set_default("url", "default")
-
- return parser
-
-def constructConfigParser():
- """
- returns a pre-setup config parser
- """
- parser = SafeConfigParser()
- parser.read([CONFIG_SYSTEM, CONFIG_USER])
- if not parser.has_section('config_file_server'):
- parser.add_section('config_file_server')
-
- return parser
-
-
-def getCombinedOptions():
- """
- Returns optparse options after it has be updated with ConfigParser
- config files and merged with parsed commandline options.
- """
- cl_parser = constructOptionParser()
- conf_parser = constructConfigParser()
-
- options, args = cl_parser.parse_args()
-
- if options.url is None:
- if conf_parser.has_option('config_file_server', 'base_host_url'):
- options.url = conf_parser.get('config_file_server', 'base_host_url')
-
- print 'USING OPTIONS:'
- print ' URL:', options.url
- print ' OUT:', options.output_filepath
- print ' FC:', options.flowcell
- print ''
-
- return options
-
-
-def saveConfigFile(flowcell, base_host_url, output_filepath):
- """
- retrieves the flowcell eland config file, give the base_host_url
- (i.e. http://sub.domain.edu:port)
- """
- url = base_host_url + '/eland_config/%s/' % (flowcell)
-
- f = open(output_filepath, 'w')
- #try:
- web = urllib.urlopen(url)
- #except IOError, msg:
- # if str(msg).find("Connection refused") >= 0:
- # print 'Error: Connection refused for: %s' % (url)
- # f.close()
- # sys.exit(1)
- # elif str(msg).find("Name or service not known") >= 0:
- # print 'Error: Invalid domain or ip address for: %s' % (url)
- # f.close()
- # sys.exit(2)
- # else:
- # raise IOError, msg
-
- data = web.read()
-
- if data.find('Hmm, config file for') >= 0:
- msg = "Flowcell (%s) not found in DB; full url(%s)" % (flowcell, url)
- raise FlowCellNotFound, msg
-
- if data.find('404 - Not Found') >= 0:
- msg = "404 - Not Found: Flowcell (%s); base_host_url (%s);\n full url(%s)\n " \
- "Did you get right port #?" % (flowcell, base_host_url, url)
- raise FlowCellNotFound, msg
-
- f.write(data)
- web.close()
- f.close()
- print 'Wrote config file to %s' % (output_filepath)
-
-
-if __name__ == '__main__':
- #Display help if no args are presented
- if len(sys.argv) == 1:
- sys.argv.append('-h')
-
- options = getCombinedOptions()
- msg_list = ['ERROR MESSAGES:']
- if options.output_filepath is None:
- msg_list.append(" Output filepath argument required. -o <filepath> or --output=<filepath>")
-
- if options.flowcell is None:
- msg_list.append(" Flow cell argument required. -f <flowcell> or --flowcell=<flowcell>")
-
- if options.url is None:
- msg_list.append(" URL argument required (-u <url> or --url=<url>), or entry\n" \
- " in /etc/elandifier/elandifer.conf or ~/.elandifier.conf")
-
- if len(msg_list) > 1:
- print '\n'.join(msg_list)
- sys.exit(0)
-
- saveConfigFile(options.flowcell, options.url, options.output_filepath)
-
--- /dev/null
+#!/usr/bin/python
+import subprocess
+import logging
+import time
+import re
+import os
+
+from gaworkflow.pipeline.retrieve_config import getCombinedOptions, saveConfigFile
+from gaworkflow.pipeline.retrieve_config import FlowCellNotFound, WebError404
+from gaworkflow.pipeline.genome_mapper import DuplicateGenome, getAvailableGenomes, constructMapperDict
+
+from pyinotify import WatchManager, ThreadedNotifier
+from pyinotify import EventsCodes, ProcessEvent
+
+logging.basicConfig(level=logging.DEBUG,
+ format='%(asctime)s %(levelname)-8s %(message)s',
+ datefmt='%a, %d %b %Y %H:%M:%S',
+ filename='pipeline_main.log',
+ filemode='w')
+
+class ConfigInfo:
+
+ def __init__(self):
+ self.run_path = None
+ self.bustard_path = None
+ self.config_filepath = None
+
+
+####################################
+# inotify event processor
+
+s_firecrest_finished = re.compile('Firecrest[0-9\._\-A-Za-z]+/finished.txt')
+s_bustard_finished = re.compile('Bustard[0-9\._\-A-Za-z]+/finished.txt')
+s_gerald_finished = re.compile('GERALD[0-9\._\-A-Za-z]+/finished.txt')
+
+class RunEvent(ProcessEvent):
+
+ def __init__(self):
+
+ self.run_status_dict = {'firecrest': False,
+ 'bustard': False,
+ 'gerald': False}
+
+ ProcessEvent.__init__(self)
+
+ def process_IN_CREATE(self, event):
+ fullpath = os.path.join(event.path, event.name)
+ if s_finished.search(fullpath):
+ logging.info("File Found: %s" % (fullpath))
+
+ if s_firecrest_finished.search(fullpath):
+ self.run_status_dict['firecrest'] = True
+ elif s_bustard_finished.search(fullpath):
+ self.run_status_dict['bustard'] = True
+ elif s_gerald_finished.search(fullpath):
+ self.run_status_dict['gerald'] = True
+
+ print "Create: %s" % (os.path.join(event.path, event.name))
+
+ def process_IN_DELETE(self, event):
+ print "Remove %s" % (os.path.join(event.path, event.name))
+
+#FLAGS
+# Config Step Error
+RUN_ABORT = 'abort'
+# Run Step Error
+RUN_FAILED = 'failed'
+
+
+#####################################
+# Configure Step (goat_pipeline.py)
+#Info
+s_start = re.compile('Starting Genome Analyzer Pipeline')
+s_gerald = re.compile("[\S\s]+--GERALD[\S\s]+--make[\S\s]+")
+s_generating = re.compile('Generating journals, Makefiles and parameter files')
+s_seq_folder = re.compile('^Sequence folder: ')
+s_seq_folder_sub = re.compile('want to make ')
+s_stderr_taskcomplete = re.compile('^Task complete, exiting')
+
+#Errors
+s_invalid_cmdline = re.compile('Usage:[\S\s]*goat_pipeline.py')
+s_species_dir_err = re.compile('Error: Lane [1-8]:')
+s_goat_traceb = re.compile("^Traceback \(most recent call last\):")
+
+
+##Ignore - Example of out above each ignore regex.
+#NOTE: Commenting out an ignore will cause it to be
+# logged as DEBUG with the logging module.
+#CF_STDERR_IGNORE_LIST = []
+s_skip = re.compile('s_[0-8]_[0-9]+')
+
+
+##########################################
+# Pipeline Run Step (make -j8 recursive)
+
+##Info
+s_finished = re.compile('finished')
+
+##Errors
+s_make_error = re.compile('^make[\S\s]+Error')
+s_no_gnuplot = re.compile('gnuplot: command not found')
+s_no_convert = re.compile('^Can\'t exec "convert"')
+s_no_ghostscript = re.compile('gs: command not found')
+
+##Ignore - Example of out above each ignore regex.
+#NOTE: Commenting out an ignore will cause it to be
+# logged as DEBUG with the logging module.
+#
+PL_STDERR_IGNORE_LIST = []
+# Info: PF 11802
+PL_STDERR_IGNORE_LIST.append( re.compile('^Info: PF') )
+# About to analyse intensity file s_4_0101_sig2.txt
+PL_STDERR_IGNORE_LIST.append( re.compile('^About to analyse intensity file') )
+# Will send output to standard output
+PL_STDERR_IGNORE_LIST.append( re.compile('^Will send output to standard output') )
+# Found 31877 clusters
+PL_STDERR_IGNORE_LIST.append( re.compile('^Found [0-9]+ clusters') )
+# Will use quality criterion ((CHASTITY>=0.6)
+PL_STDERR_IGNORE_LIST.append( re.compile('^Will use quality criterion') )
+# Quality criterion translated to (($F[5]>=0.6))
+PL_STDERR_IGNORE_LIST.append( re.compile('^Quality criterion translated to') )
+# opened /woldlab/trog/data1/king/070924_USI-EAS44_0022_FC12150/Data/C1-36_Firecrest1.9.1_14-11-2007_king.4/Bustard1.9.1_14-11-2007_king/s_4_0101_qhg.txt
+# AND
+# opened s_4_0103_qhg.txt
+PL_STDERR_IGNORE_LIST.append( re.compile('^opened[\S\s]+qhg.txt') )
+# 81129 sequences out of 157651 passed filter criteria
+PL_STDERR_IGNORE_LIST.append( re.compile('^[0-9]+ sequences out of [0-9]+ passed filter criteria') )
+
+
+def pl_stderr_ignore(line):
+ """
+ Searches lines for lines to ignore (i.e. not to log)
+
+ returns True if line should be ignored
+ returns False if line should NOT be ignored
+ """
+ for s in PL_STDERR_IGNORE_LIST:
+ if s.search(line):
+ return True
+ return False
+
+
+def config_stdout_handler(line, conf_info):
+ """
+ Processes each line of output from GOAT
+ and stores useful information using the logging module
+
+ Loads useful information into conf_info as well, for future
+ use outside the function.
+
+ returns True if found condition that signifies success.
+ """
+
+ # Skip irrelevant line (without logging)
+ if s_skip.search(line):
+ pass
+
+ # Detect invalid command-line arguments
+ elif s_invalid_cmdline.search(line):
+ logging.error("Invalid commandline options!")
+
+ # Detect starting of configuration
+ elif s_start.search(line):
+ logging.info('START: Configuring pipeline')
+
+ # Detect it made it past invalid arguments
+ elif s_gerald.search(line):
+ logging.info('Running make now')
+
+ # Detect that make files have been generated (based on output)
+ elif s_generating.search(line):
+ logging.info('Make files generted')
+ return True
+
+ # Capture run directory
+ elif s_seq_folder.search(line):
+ mo = s_seq_folder_sub.search(line)
+ #Output changed when using --tiles=<tiles>
+ # at least in pipeline v0.3.0b2
+ if mo:
+ firecrest_bustard_gerald_makefile = line[mo.end():]
+ firecrest_bustard_gerald, junk = \
+ os.path.split(firecrest_bustard_gerald_makefile)
+ firecrest_bustard, junk = os.path.split(firecrest_bustard_gerald)
+ firecrest, junk = os.path.split(firecrest_bustard)
+
+ conf_info.bustard_path = firecrest_bustard
+ conf_info.run_path = firecrest
+
+ #Standard output handling
+ else:
+ print 'Sequence line:', line
+ mo = s_seq_folder.search(line)
+ conf_info.bustard_path = line[mo.end():]
+ conf_info.run_path, temp = os.path.split(conf_info.bustard_path)
+
+ # Log all other output for debugging purposes
+ else:
+ logging.warning('CONF:?: %s' % (line))
+
+ return False
+
+
+
+def config_stderr_handler(line, conf_info):
+ """
+ Processes each line of output from GOAT
+ and stores useful information using the logging module
+
+ Loads useful information into conf_info as well, for future
+ use outside the function.
+
+ returns RUN_ABORT upon detecting failure;
+ True on success message;
+ False if neutral message
+ (i.e. doesn't signify failure or success)
+ """
+
+ # Detect invalid species directory error
+ if s_species_dir_err.search(line):
+ logging.error(line)
+ return RUN_ABORT
+ # Detect goat_pipeline.py traceback
+ elif s_goat_traceb.search(line):
+ logging.error("Goat config script died, traceback in debug output")
+ return RUN_ABORT
+ # Detect indication of successful configuration (from stderr; odd, but ok)
+ elif s_stderr_taskcomplete.search(line):
+ logging.info('Configure step successful (from: stderr)')
+ return True
+ # Log all other output as debug output
+ else:
+ logging.debug('CONF:STDERR:?: %s' % (line))
+
+ # Neutral (not failure; nor success)
+ return False
+
+
+#def pipeline_stdout_handler(line, conf_info):
+# """
+# Processes each line of output from running the pipeline
+# and stores useful information using the logging module
+#
+# Loads useful information into conf_info as well, for future
+# use outside the function.
+#
+# returns True if found condition that signifies success.
+# """
+#
+# #f.write(line + '\n')
+#
+# return True
+
+
+
+def pipeline_stderr_handler(line, conf_info):
+ """
+ Processes each line of stderr from pipelien run
+ and stores useful information using the logging module
+
+ ##FIXME: Future feature (doesn't actually do this yet)
+ #Loads useful information into conf_info as well, for future
+ #use outside the function.
+
+ returns RUN_FAILED upon detecting failure;
+ #True on success message; (no clear success state)
+ False if neutral message
+ (i.e. doesn't signify failure or success)
+ """
+
+ if pl_stderr_ignore(line):
+ pass
+ elif s_make_error.search(line):
+ logging.error("make error detected; run failed")
+ return RUN_FAILED
+ elif s_no_gnuplot.search(line):
+ logging.error("gnuplot not found")
+ return RUN_FAILED
+ elif s_no_convert.search(line):
+ logging.error("imagemagick's convert command not found")
+ return RUN_FAILED
+ elif s_no_ghostscript.search(line):
+ logging.error("ghostscript not found")
+ return RUN_FAILED
+ else:
+ logging.debug('PIPE:STDERR:?: %s' % (line))
+
+ return False
+
+
+def retrieve_config(conf_info, flowcell, cfg_filepath, genome_dir):
+ """
+ Gets the config file from server...
+ requires config file in:
+ /etc/ga_frontend/ga_frontend.conf
+ or
+ ~/.ga_frontend.conf
+
+ with:
+ [config_file_server]
+ base_host_url: http://host:port
+
+ return True if successful, False is failure
+ """
+ options = getCombinedOptions()
+
+ if options.url is None:
+ logging.error("~/.ga_frontend.conf or /etc/ga_frontend/ga_frontend.conf" \
+ " missing base_host_url option")
+ return False
+
+ try:
+ saveConfigFile(flowcell, options.url, cfg_filepath)
+ conf_info.config_filepath = cfg_filepath
+ except FlowCellNotFound, e:
+ logging.error(e)
+ return False
+ except WebError404, e:
+ logging.error(e)
+ return False
+ except IOError, e:
+ logging.error(e)
+ return False
+ except Exception, e:
+ logging.error(e)
+ return False
+
+ f = open(cfg_filepath, 'r')
+ data = f.read()
+ f.close()
+
+ genome_dict = getAvailableGenomes(genome_dir)
+ mapper_dict = constructMapperDict(genome_dict)
+
+ f = open(cfg_filepath, 'w')
+ f.write(data % (mapper_dict))
+ f.close()
+
+ return True
+
+
+
+def configure(conf_info):
+ """
+ Attempts to configure the GA pipeline using goat.
+
+ Uses logging module to store information about status.
+
+ returns True if configuration successful, otherwise False.
+ """
+ #ERROR Test:
+ #pipe = subprocess.Popen(['goat_pipeline.py',
+ # '--GERALD=config32bk.txt',
+ # '--make .',],
+ # #'.'],
+ # stdout=subprocess.PIPE,
+ # stderr=subprocess.PIPE)
+
+ #ERROR Test (2), causes goat_pipeline.py traceback
+ #pipe = subprocess.Popen(['goat_pipeline.py',
+ # '--GERALD=%s' % (conf_info.config_filepath),
+ # '--tiles=s_4_100,s_4_101,s_4_102,s_4_103,s_4_104',
+ # '--make',
+ # '.'],
+ # stdout=subprocess.PIPE,
+ # stderr=subprocess.PIPE)
+
+ ##########################
+ # Run configuration step
+ # Not a test; actual configure attempt.
+ #pipe = subprocess.Popen(['goat_pipeline.py',
+ # '--GERALD=%s' % (conf_info.config_filepath),
+ # '--make',
+ # '.'],
+ # stdout=subprocess.PIPE,
+ # stderr=subprocess.PIPE)
+
+ # CONTINUE HERE
+ #FIXME: this only does a run on 5 tiles on lane 4
+ pipe = subprocess.Popen(['goat_pipeline.py',
+ '--GERALD=%s' % (conf_info.config_filepath),
+ '--tiles=s_4_0100,s_4_0101,s_4_0102,s_4_0103,s_4_0104',
+ '--make',
+ '.'],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE)
+ ##################
+ # Process stdout
+ stdout_line = pipe.stdout.readline()
+
+ complete = False
+ while stdout_line != '':
+ # Handle stdout
+ if config_stdout_handler(stdout_line, conf_info):
+ complete = True
+ stdout_line = pipe.stdout.readline()
+
+
+ error_code = pipe.wait()
+ if error_code:
+ logging.error('Recieved error_code: %s' % (error_code))
+ else:
+ logging.info('We are go for launch!')
+
+ #Process stderr
+ stderr_line = pipe.stderr.readline()
+
+ abort = 'NO!'
+ stderr_success = False
+ while stderr_line != '':
+ stderr_status = config_stderr_handler(stderr_line, conf_info)
+ if stderr_status == RUN_ABORT:
+ abort = RUN_ABORT
+ elif stderr_status is True:
+ stderr_success = True
+ stderr_line = pipe.stderr.readline()
+
+
+ #Success requirements:
+ # 1) The stdout completed without error
+ # 2) The program exited with status 0
+ # 3) No errors found in stdout
+ print '#Expect: True, False, True, True'
+ print complete, bool(error_code), abort != RUN_ABORT, stderr_success is True
+ status = complete is True and \
+ bool(error_code) is False and \
+ abort != RUN_ABORT and \
+ stderr_success is True
+
+ # If everything was successful, but for some reason
+ # we didn't retrieve the path info, log it.
+ if status is True:
+ if conf_info.bustard_path is None or conf_info.run_path is None:
+ logging.error("Failed to retrieve run_path")
+ return False
+
+ return status
+
+
+def run_pipeline(conf_info):
+ """
+ Run the pipeline and monitor status.
+ """
+ # Fail if the run_path doesn't actually exist
+ if not os.path.exists(conf_info.run_path):
+ logging.error('Run path does not exist: %s' \
+ % (conf_info.run_path))
+ return False
+
+ # Change cwd to run_path
+ os.chdir(conf_info.run_path)
+ stdout_filepath = os.path.join(conf_info.run_path, 'pipeline_run_stdout.txt')
+ stderr_filepath = os.path.join(conf_info.run_path, 'pipeline_run_stderr.txt')
+
+ # Monitor file creation
+ wm = WatchManager()
+ mask = EventsCodes.IN_DELETE | EventsCodes.IN_CREATE
+ event = RunEvent()
+ notifier = ThreadedNotifier(wm, event)
+ notifier.start()
+ wdd = wm.add_watch(conf_info.run_path, mask, rec=True)
+
+ # Log pipeline starting
+ logging.info('STARTING PIPELINE @ %s' % (time.ctime()))
+
+ # Start the pipeline (and hide!)
+ #pipe = subprocess.Popen(['make',
+ # '-j8',
+ # 'recursive'],
+ # stdout=subprocess.PIPE,
+ # stderr=subprocess.PIPE)
+
+ fout = open(stdout_filepath, 'w')
+ ferr = open(stderr_filepath, 'w')
+
+ pipe = subprocess.Popen(['make',
+ '-j8',
+ 'recursive'],
+ stdout=fout,
+ stderr=ferr)
+ #shell=True)
+ # Wait for run to finish
+ retcode = pipe.wait()
+
+
+ # Clean up
+ notifier.stop()
+ fout.close()
+ ferr.close()
+
+ # Process stderr
+ ferr = open(stderr_filepath, 'r')
+
+ run_failed_stderr = False
+ for line in ferr:
+ err_status = pipeline_stderr_handler(line, conf_info)
+ if err_status == RUN_FAILED:
+ run_failed_stderr = True
+
+ ferr.close()
+
+ # Finished file check!
+ print 'RUN SUCCESS CHECK:'
+ for key, value in event.run_status_dict.items():
+ print ' %s: %s' % (key, value)
+
+ dstatus = event.run_status_dict
+
+ # Success or failure check
+ status = (retcode == 0) and \
+ run_failed_stderr is False and \
+ dstatus['firecrest'] is True and \
+ dstatus['bustard'] is True and \
+ dstatus['gerald'] is True
+
+ return status
+
+
--- /dev/null
+#!/usr/bin/python
+import glob
+import sys
+import os
+
+import logging
+
+class DuplicateGenome(Exception): pass
+
+
+def _has_metainfo(genome_dir):
+ metapath = os.path.join(genome_dir, '_metainfo_')
+ if os.path.isfile(metapath):
+ return True
+ else:
+ return False
+
+def getAvailableGenomes(genome_base_dir):
+ """
+ raises IOError (on genome_base_dir not found)
+ raises DuplicateGenome on duplicate genomes found.
+
+ returns a double dictionary (i.e. d[species][build] = path)
+ """
+
+ # Need valid directory
+ if not os.path.exists(genome_base_dir):
+ msg = "Directory does not exist: %s" % (genome_base_dir)
+ raise IOError, msg
+
+ # Find all subdirectories
+ filepath_list = glob.glob(os.path.join(genome_base_dir, '*'))
+ potential_genome_dirs = \
+ [ filepath for filepath in filepath_list if os.path.isdir(filepath)]
+
+ # Get list of metadata files
+ genome_dir_list = \
+ [ dirpath \
+ for dirpath in potential_genome_dirs \
+ if _has_metainfo(dirpath) ]
+
+ # Genome double dictionary
+ d = {}
+
+ for genome_dir in genome_dir_list:
+ line = open(os.path.join(genome_dir, '_metainfo_'), 'r').readline().strip()
+
+ # Get species, build... log and skip on failure
+ try:
+ species, build = line.split('|')
+ except:
+ logging.warning('Skipping: Invalid metafile (%s) line: %s' \
+ % (metafile, line))
+ continue
+
+ build_dict = d.setdefault(species, {})
+ if build in build_dict:
+ msg = "Duplicate genome for %s|%s" % (species, build)
+ raise DuplicateGenome, msg
+
+ build_dict[build] = genome_dir
+
+ return d
+
+
+def constructMapperDict(genome_dict):
+ """
+ Creates a dictionary which can map the genome
+ in the eland config generator output to a local
+ genome path
+
+ ie. 'Homo sapiens|hg18' -> <genome_dir>
+ """
+ mapper_dict = {}
+ for species in genome_dict.keys():
+ for build in genome_dict[species]:
+ mapper_dict[species+'|'+build] = genome_dict[species][build]
+
+ return mapper_dict
+
+
+if __name__ == '__main__':
+
+ if len(sys.argv) != 2:
+ print 'useage: %s <base_genome_dir>' % (sys.argv[0])
+ sys.exit(1)
+
+ d = getAvailableGenomes(sys.argv[1])
+ d2 = constructMapperDict(d)
+
+ for k,v in d2.items():
+ print '%s: %s' % (k,v)
+
+
--- /dev/null
+#!/usr/bin/env python
+
+from optparse import OptionParser, IndentedHelpFormatter
+from ConfigParser import SafeConfigParser
+
+import os
+import sys
+import urllib
+
+CONFIG_SYSTEM = '/etc/ga_frontend/ga_frontend.conf'
+CONFIG_USER = os.path.expanduser('~/.ga_frontend.conf')
+
+
+class FlowCellNotFound(Exception): pass
+class WebError404(Exception): pass
+
+
+class PreformattedDescriptionFormatter(IndentedHelpFormatter):
+
+ #def format_description(self, description):
+ #
+ # if description:
+ # return description + "\n"
+ # else:
+ # return ""
+
+ def format_epilog(self, epilog):
+ """
+ It was removing my preformated epilog, so this should override
+ that behavior! Muhahaha!
+ """
+ if epilog:
+ return "\n" + epilog + "\n"
+ else:
+ return ""
+
+
+def constructOptionParser():
+ """
+ returns a pre-setup optparser
+ """
+ parser = OptionParser(formatter=PreformattedDescriptionFormatter())
+
+ parser.set_description('Retrieves eland config file from ga_frontend web frontend.')
+
+ parser.epilog = """
+Config File:
+ * %s (System wide)
+ * %s (User specific; overrides system)
+ * command line overrides all config file options
+
+ Example Config File:
+
+ [server_info]
+ base_host_url=http://somewhere.domain:port
+""" % (CONFIG_SYSTEM, CONFIG_USER)
+
+ #Special formatter for allowing preformatted description.
+ ##parser.format_epilog(PreformattedDescriptionFormatter())
+
+ parser.add_option("-u", "--url",
+ action="store", type="string", dest="url")
+
+ parser.add_option("-o", "--output",
+ action="store", type="string", dest="output_filepath")
+
+ parser.add_option("-f", "--flowcell",
+ action="store", type="string", dest="flowcell")
+
+ #parser.set_default("url", "default")
+
+ return parser
+
+def constructConfigParser():
+ """
+ returns a pre-setup config parser
+ """
+ parser = SafeConfigParser()
+ parser.read([CONFIG_SYSTEM, CONFIG_USER])
+ if not parser.has_section('config_file_server'):
+ parser.add_section('config_file_server')
+
+ return parser
+
+
+def getCombinedOptions():
+ """
+ Returns optparse options after it has be updated with ConfigParser
+ config files and merged with parsed commandline options.
+ """
+ cl_parser = constructOptionParser()
+ conf_parser = constructConfigParser()
+
+ options, args = cl_parser.parse_args()
+
+ if options.url is None:
+ if conf_parser.has_option('config_file_server', 'base_host_url'):
+ options.url = conf_parser.get('config_file_server', 'base_host_url')
+
+ print 'USING OPTIONS:'
+ print ' URL:', options.url
+ print ' OUT:', options.output_filepath
+ print ' FC:', options.flowcell
+ print ''
+
+ return options
+
+
+def saveConfigFile(flowcell, base_host_url, output_filepath):
+ """
+ retrieves the flowcell eland config file, give the base_host_url
+ (i.e. http://sub.domain.edu:port)
+ """
+ url = base_host_url + '/eland_config/%s/' % (flowcell)
+
+ f = open(output_filepath, 'w')
+ #try:
+ web = urllib.urlopen(url)
+ #except IOError, msg:
+ # if str(msg).find("Connection refused") >= 0:
+ # print 'Error: Connection refused for: %s' % (url)
+ # f.close()
+ # sys.exit(1)
+ # elif str(msg).find("Name or service not known") >= 0:
+ # print 'Error: Invalid domain or ip address for: %s' % (url)
+ # f.close()
+ # sys.exit(2)
+ # else:
+ # raise IOError, msg
+
+ data = web.read()
+
+ if data.find('Hmm, config file for') >= 0:
+ msg = "Flowcell (%s) not found in DB; full url(%s)" % (flowcell, url)
+ raise FlowCellNotFound, msg
+
+ if data.find('404 - Not Found') >= 0:
+ msg = "404 - Not Found: Flowcell (%s); base_host_url (%s);\n full url(%s)\n " \
+ "Did you get right port #?" % (flowcell, base_host_url, url)
+ raise FlowCellNotFound, msg
+
+ f.write(data)
+ web.close()
+ f.close()
+ print 'Wrote config file to %s' % (output_filepath)
+
+
--- /dev/null
+#!/usr/bin/env python
+import sys
+from gaworkflow.pipeline.configure_run import *
+
+def main(args=None):
+ ci = ConfigInfo()
+
+ flowcell = 'FC12150'
+ cfg_filepath = 'config32auto.txt'
+ genome_dir = '/home/king/trog_drive/'
+
+ status_retrieve_cfg = retrieve_config(ci, flowcell, cfg_filepath, genome_dir)
+ if status_retrieve_cfg:
+ print "Retrieve config file successful"
+ else:
+ print "Failed to retrieve config file"
+ #ci.config_filepath = 'config32bk.txt'
+
+ if status_retrieve_cfg:
+ status = configure(ci)
+ if status:
+ print "Configure success"
+ else:
+ print "Configure failed"
+
+ print 'Run Dir:', ci.run_path
+ print 'Bustard Dir:', ci.bustard_path
+
+ if status:
+ print 'Running pipeline now!'
+ run_status = run_pipeline(ci)
+ if run_status is True:
+ print 'Pipeline ran successfully.'
+ return 0
+ else:
+ print 'Pipeline run failed.'
+ return 1
+
+ return 2
+
+if __name__ == "__main__":
+ sys.exit(main(sys.argv[1:]))
--- /dev/null
+#!/usr/bin/env python
+import sys
+from gaworkflow.pipeline.retrieve_config import *
+
+def main(args=None):
+ #Display help if no args are presented
+ if len(sys.argv) == 1:
+ sys.argv.append('-h')
+
+ options = getCombinedOptions()
+ msg_list = ['ERROR MESSAGES:']
+ if options.output_filepath is None:
+ msg_list.append(" Output filepath argument required. -o <filepath> or --output=<filepath>")
+
+ if options.flowcell is None:
+ msg_list.append(" Flow cell argument required. -f <flowcell> or --flowcell=<flowcell>")
+
+ if options.url is None:
+ msg_list.append(" URL argument required (-u <url> or --url=<url>), or entry\n" \
+ " in /etc/elandifier/elandifer.conf or ~/.elandifier.conf")
+
+ if len(msg_list) > 1:
+ print '\n'.join(msg_list)
+ return 1
+
+ saveConfigFile(options.flowcell, options.url, options.output_filepath)
+ return 0
+
+if __name__ == "__main__":
+ sys.exit(main(sys.argv[1:]))
author="Diane Trout",
author_email="diane@caltech.edu",
packages=["uashelper"],
- scripts=['scripts/spoolwatcher', 'scripts/copier'],
+ scripts=['scripts/spoolwatcher',
+ 'scripts/copier',
+ 'scripts/retreive_config',
+ 'scripts/configure_pipeline'],
)
projects / htsworkflow.git / commitdiff