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import os , os.path
# this a python module the syntax used is the python syntax
############################################
# #
# Mandatory values #
# #
############################################
# the root url of mobyle
# warning: do NOT include the port number if it is 80, it is useless
# and creates problems on the server
ROOT_URL = "http://localhost"
#base project url for mobyle cgis = ROOT_URL + CGI_PREFIX
CGI_PREFIX = 'cgi-bin/mobyle'
#base project url for mobyle htdocs = ROOT_URL + HTDOCS_PREFIX
HTDOCS_PREFIX = 'mobyle'
#########
# #
# mails #
# #
#########
#a list of email addresses who will received messages when problems occur
MAINTAINER = [ "name@mydommain.fr" ]
#a list of email addresses where the users could have help on this Mobyle portal
HELP= [ "name2@mydommain.fr" , "name3@mydommain.fr" ]
# local mailhost
MAILHOST= "mailhost.mydommain.fr"
##################
# #
# queuing system #
# #
##################
from Execution import *
#EXECUTION_SYSTEM_ALIAS = {
# 'DRMAA_sge' : SgeDRMAAConfig( '/path/to/sge/libdrmaa.so' ,
# root = 'path to sge root',
# cell = 'cell name' ) ,
# 'DRMAA_torque': PbsDRMAAConfig( '/path/to/torque-pbs/libdrmaa.so' ,
# 'marygay.sis.pasteur.fr' ),
# 'SGE' : SGEConfig( root = '/path/to/sge_root',
# cell= 'cell name' ) ,
# 'SYS' : SYSConfig() ,
# 'LSF' : LsfDRMAAConfig( '/path/to/LSF/libdrmaa.so' ,
# lsf_envdir = 'the contained of LSF_ENVDIR' ,
# lsf_serverdir = 'the contained of LSF_SERVERDIR')
# }
EXECUTION_SYSTEM_ALIAS = { 'SYS' : SYSConfig() }
from Mobyle.Dispatcher import DefaultDispatcher
#DISPATCHER = DefaultDispatcher( {
# 'service1' : ( EXECUTION_SYSTEM_ALIAS[ 'DRMAA_sge' ] , 'queue name' ),
# 'service2' : ( EXECUTION_SYSTEM_ALIAS[ 'DRMAA_torque' ] , 'queue name' ),
# 'service3' : ( EXECUTION_SYSTEM_ALIAS[ 'LSF' ] , 'queue name' ),
# 'service4' : ( EXECUTION_SYSTEM_ALIAS[ 'SGE' ] , 'queue name' ),
# 'service5' : ( EXECUTION_SYSTEM_ALIAS[ 'DRMAA_sge' ] , 'queue name' ),
# 'DEFAULT' : ( EXECUTION_SYSTEM_ALIAS[ 'SYS' ] , '' )
# } )
DISPATCHER = DefaultDispatcher( { 'DEFAULT' : ( EXECUTION_SYSTEM_ALIAS[ 'SYS' ] , '' ) } )
#######################
# #
# logging #
# #
#######################
#the directory were will stored the log files
LOGDIR = '/var/log/mobyle/'
####################################################
# #
# data format detection and conversion #
# #
####################################################
# for Sequence and Alignment, the HIGHLY recommended squizz converters
# are available
#DATA_CONVERTER={
# 'Datatype1': [converter_class1(path_to_the_corresponding_converter_program), converter_class2(path)],
# 'Datatype2': [converter_class1(path_to_the_corresponding_converter_program), converter_class2(path)]
# }
from Mobyle.Converter import *
DATA_CONVERTER={
'Sequence': [ squizz_sequence('/usr/bin/squizz') ] ,
'Alignment': [ squizz_alignment('/usr/bin/squizz'),
fasta_phyml(None),
phylipi_phyml(None),
phylips_phyml(None),
clustal_phyml(None),
nexus_phyml(None),
stockholm_phyml(None)]
}
########################################################################
########################################################################
## ##
## Optionals Values ##
## ##
########################################################################
########################################################################
#########
# #
# Debug #
# #
#########
#used in production
# 0 - the command line is build
# - the build log is NOT fill
# - the job is executed
#to test a xml ( python syntax in code , precond ... )
# 1 - the command line is build
# - the build log is NOT fill
# - the job is NOT executed
#to know what's wrong in the xml I wrote.
# 2 - the command line is build
# - the build log is fill
# - the job is NOT executed
#to test the xml and the job execution and the results retrieving
# 3 - the command line is build
# - the build log is fill
# - the job is executed
DEBUG = 3
#to set a different debug level for a particular service
#PARTICULAR_DEBUG = { 'serviceName' : 3 }
###############
# #
# Directories #
# #
###############
## were are the binary corresponding to the services
## a list of string
## each element must be a valid path
## the element order is kept to build the final PATH ( the binary path is add before the canonical PATH )
BINARY_PATH = ["/usr/local/bin","/usr/lib/phylip/bin"]
#DATABANKS_CONFIG = {
# 'wgs':{
# 'dataType' : 'Sequence',
# 'bioTypes' : ['Nucleic'],
# 'label' : 'Genbank - Whole Genome Shotgun',
# 'command': ['golden', '%(db)s:%(id)s']
# },
# 'pdb':{
# 'dataType':'3DStructure',
# 'bioTypes':['Protein'],
# 'label': 'Protein Data Bank',
# 'command': [ "/path/to/PDBGet.py", "%(id)s" ]
# }
# }
DATABANKS_CONFIG = {}
#####################
#
# Statistics
#
#####################
## Google Analytics code - set to use GA
#GACODE = 'XXXXXXXXXX'
######################
# #
# Authentication #
# #
######################
## Enable OpenID
# default value = False
# OPENID = True
#####################
#
# Welcome page configuration
#
#####################
## news_ex illustrating example feed is in Example/Local directory.
#WELCOME_CONFIG = {'url':'http://localhost:85/portal/news_ex.atom',
# 'format':'atom'}
#####################
#
# Portal custom content for header and footer
#
#####################
#
#CUSTOM_PORTAL_HEADER="<h1>myOwnPortalName</h1>"
#
#CUSTOM_PORTAL_FOOTER="<div>insert the name of your sponsors or your legal disclaimers</div>
## to make email optional for all programs, set this to True
## default value = False
#OPT_EMAIL = False
## to have a more control on the mandatory email
## it able to have the general option but
## it could be set to another value for particular service
## example :
## OPT_EMAIL could be set at False ( the email is mandatory )
## but set a True for some very short services.
# the key is the portal id of a service and value is a boolean
# for local services the portal id the server name can be ommited
# eg 'local.golden' == 'golden'
#PARTICULAR_OPT_EMAIL = {'portal_id' : True }
#if a job is longer than EMAIL_DELAY Mobyle send the results by email (if user give it's email)
#its express in second, 0 mean no email (default = 60)
#EMAIL_DELAY = 60
## anonymous session there is 3 available values
## 'no' : the anonymous sessions are not allowed
## 'yes' : the anonymous sessions are allowed, without any verification
## 'captcha' : the anonymous sessions are allowed, but with a captcha challenge ( default )
#ANONYMOUS_SESSION = "captcha"
## authenticated session there is 3 available values
## 'no' : the authenticated session are not allowed.
## 'yes' : the authenticated session are allowed and activated without any restriction.
## 'email' : the authenticated session are allowed but an email confirmation is needed to activate it (default).
#AUTHENTICATED_SESSION = "email"
##############
# #
# misc #
# #
##############
## the time to consider that a job is long ( in sec default = 60 , min = 10 )
#TIMEOUT = 60
## refresh frequency for user data in the web portal, in seconds
## default: 240
#REFRESH_FREQUENCY = 240
## max size for any file (2 Go )
#this limit is honored only if the EXECUTION_SYSTEM_ALIAS is set to Sys (SYSConfig)
#if SGE, PBS, ... is used this must be set directly in the drm configuration.
#FILELIMIT = 2147483648
## max size for a session in bytes ( default = 50Mo = 52428800 )
#SESSIONLIMIT = 52428800
##max size to preview the results
##if the results size exceed this limit the results appear as a link ( default value = 1048576 = 1Mib )
#PREVIEW_DATA_LIMIT = 1048576
#the number of "similar" jobs a user is allowed to submit at a given time.
#similar means same email, same command line. ( default = 1 )
#0 disable this control, then the user may submit as many "same" jobs he wants.
#if the email is not provided (depend of the configuration) this control is disabled.
# !! this new directive replace SIMULTANEOUS_JOBS !!
#MAX_SIMILAR_JOB_PER_USER =1
#the number of jobs than a user can submit at a given time
#0 disable this control, then the user may submit as many "same" jobs he wants (default).
#if the email is not provided (depend of the configuration) this control is disabled.
#MAX_JOB_PER_USER = 0
##########
# #
# Mail #
# #
##########
##from: sender email address ( default = HELP )
#SENDER = "myname-noreply@mydomain.fr"
##set this True if you don't want results to be sent by email.
##This does not make email optional
#DONT_EMAIL_RESULTS = False
## max size for results by email ( in bytes default 2 Mib )
#MAXMAILSIZE = 2097152
## how long should results be available on the server ( in days default = 10)?
#RESULT_REMAIN = 10
## if you want to resolve the domain name of the user email
## and if it has a mail exchanger field
## (to avoid fake user email address)
## by default DNS_RESOLVER = False
## if DNS_RESOLVER = True dnspython must be installed
#DNS_RESOLVER = False
################
# #
# logging #
# #
################
## to monitored the elapsed time per job ( default = False )
#ACCOUNTING = True
#######################
# #
# disabling services #
# #
#######################
## some times you need to disable the portal for maintaining operation etc...
## if DISABLE_ALL is True no new job could be submit, but the running job keep running
#DISABLE_ALL = False
## To disable specifically one service (program or workflow) from any portal, you can append it in DISABLED_SERVICES.
## joker can be used, so it's easy to disable all services from a given portal.
## this portal is call 'local'
## to re-enable services just toggle DISABLE_ALL to False or remove it from
## the DISABLED_SERVICES list
## example:
##DISABLED_SERVICES = [ 'portal1.service1' , # disable the service1 from the imported portal1 (as defined in PORTALS )
## 'portal2.*' , # disable all services from the imported portal2
## 'local.clustalw*' # disable all services begining by clustalw (clutalw-multialign ,clustalw-sequence , clustalw-profile ) from this server.
## ]
## By default all services are enabled
#DISABLED_SERVICES = []
################################
# #
# restriction services access #
# #
################################
## by default all the programs available are usable by all
## users who can access your web server. but sometimes,due to
## some license restrictions etc... , you need to restrict the
## accessibility of some programs to some users.
## to do that use the AUTHORIZED_SERVICES
## The filtering is based on the ip of the requester.
## AUTHORIZED_SERVICES is a dictionary with the service names of
## programs to restrict as keys and the list of ip which can
## access these programs as values
##
## AUTHORIZED_SERVICES = { serviceURL :[ ip , ip mask ] }
##
## the ip address which can use the service
##
## AUTHORIZED_SERVICES = 'http://myMobyle.mydomain.fr/data/programs/toppred.xml' : [ '125.234.60.18' , # only the machine with this ip could access to toppred
## '125.234.60.*' , # all the machines in subnet could access to toppred
## '125.234.*.15 , # all the machine
## ]
##
## if there is no entry for a service it's mean that
## every body can access to this service
#AUTHORIZED_SERVICES = {}
################################
# #
# Services Management #
# #
################################
##################################################################################
# #
# Local program publishing section #
# #
# This configuration file is used to deploy the xml services descriptions on #
# the Mobyle web part from the Local/Services/* and /Srevices/* directories. #
# all the xml from Local/Services/*/* are deployed #
# the xml from Services/*/* are filtered following the rules below #
# (for more explanations see INSTALL notes and Tools/README) #
# #
# (if this file doesn't exist all the programs from Programs will be published) #
# #
##################################################################################
#the list of programs to deploy is established by filtering the Local/Services/ repository and Services repository
#with the LOCAL_DEPLOY_INCLUDE following the LOCAL_DEPLOY_EXCLUDE.
#each value corresponds to a unix mask to filter a directory, so the unix joker * can be used.
#LOCAL_DEPLOY_INCLUDE = { 'programs' : [ 'blast*' ] , #all programs definitions begining by blast will be deployed
# 'workflows': [ '*' ] , #all workflows will be deployed
# 'viewers' : [ 'jalview' , 'varna' ] , #only jalview and varna will be deployed
# }
#LOCAL_DEPLOY_EXCLUDE = { 'programs' : [ 'blast2mydb' ] , #blast2mydb will be removed from the list of programs to deploy
# 'workflows': [ '' ] ,
# 'viewers' : [ '' ] ,
# }
LOCAL_DEPLOY_INCLUDE = { 'programs' : [ '*' ] ,
'workflows': [ '*' ] ,
'viewers' : [ '*' ] ,
}
LOCAL_DEPLOY_EXCLUDE = { 'programs' : [ '' ] ,
'workflows': [ '' ] ,
'viewers' : [ '' ] ,
}
######################
# #
# Grid aspects #
# #
######################
# PORTAL_NAME is the name of the portal as it is known to others in a MobyleNet network
#PORTAL_NAME = "my_server"
# SIMPLE_FORMS activates the display of simple forms by default
# inactive by default
#SIMPLE_FORMS = False
#PORTALS={'portal1': {
# 'url': 'http://otherdomain.fr:port/cgi-bin/MobylePortal',
# 'help' : 'help@otherdomain.fr',
# 'repository': 'http://otherdomain.fr:port/',
# 'services': { 'programs' : ['clustalw-multialign'],
# 'workflows': [ 'wokflow1_of_portal1']
# }
# }
PORTALS={}
#EXPORTED_SERVICES = [ 'golden', 'abiview' ]
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