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="

myOwnPortalName

" # #CUSTOM_PORTAL_FOOTER="
insert the name of your sponsors or your legal disclaimers
## 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' ]