Configured for http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby
Check these links:
RDF directory web access: http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby/rdf/
CGI directory web access and ExecCGI option: http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby/cgi/index.cgi
If CGI script is not executed, you should modify your apache httpd.conf file (you must be root/sudoer).
Then, add a ScripAlias directive :
|ScriptAlias /biomoby/playmoby/cgi/ "/www/www-bioinfo/biomoby/playmoby/cgi/"|
PlayMOBY is governed by the CeCILL license under French law.
PlayMOBY tarball is available at the following address:
If you want to be informed about main updates, please send an email to Sebastien Carrere
First of all, a little word on how we consider webservices: for us, it is just a script/executable wrapping.
That's why our webservices are based on a system call of a standalone script handling infiles and outfiles.
By this way, we can continue to use these programs using command line call, or embed them into programming pipeline or CGIs.
Deploying a webservice using PlayMOBY is a three step protocol.
The first one, is to generate/get a Mobyle description of your executable. One aim of Mobyle project (C.Letondal et al.) is to describe any program using XML language. As for an example, they plan to describe all EMBOSS suite programs like they have done before with Pise.
So we collaborate with the Mobyle team to fit our needs.
We developped a perl module called Appli.pm to generate easily a Mobyle valid XML file; the description of your program is embedded into the program itself and is structured into perl hashes.
The main constraints are:
The second step consists in analyse the Mobyle data to principally generate a configuration file.
We choose to use a pivot format to avoid direct dependancies with Mobyle: by this way, if Mobyle specifications move in the future, we will just have to modify our Mobyle to configuration file parser without modify the third part protocol (see below).
The third part is the publication and the test of the new webservice. Here again, we choose to separate this step from the previous one in order to be more robust according to the BioMOBY's specifications evolutions.
We use two different webservice templates (synchronous one [doc]and asynchronous one [doc]) to write the perl module.
The generated webservice (the perl module and a configuration file) has to be under the PlayMOBY environment control to be available.
When you install PlayMOBY environnement for the first time you have to configure it.
The script pmb_configure.pl will modify many files (config files, perl modules) to tune PlayMOBY according to your system.
It will also check your system configuration (perl modules, binaries).
--http_path: Your PlayMOBY URL this is the "apache path" to the PlayMOBY directory; because of webservice technology , the rest of the world should access to this directory using http protocol, and especially "rdf" directory and "cgi/dispatcher.cgi" should be accessible NB1: do not forget to add ExecCGI option onto "cgi" directory NB2: try to access these directories using a web browser (using http_path root URL) from an external IP class (to avoid problems of security access) RDF directory: http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby/rdf/ CGI directory: http://lipm-bioinfo.toulouse.inra.fr/biomoby/playmoby/cgi/index.cgi --email : this PlayMoby instance administrator email --auth_uri: the authority URI is a signature for your Webservices deployed under one instance of PlayMOBY --timeout : the timeout parameter corresponds to the SOAP request Time out (in minutes) (LWP::UserAgent timeout) ; by default, we use 10 minutes there's also another timeout in your apache server, so take care to be synchronized with this one if you want to modify apache timeout, contact your administrator (maybe he should prefer to use a virtual host with specific timeout) --unix_path: the full path where you untar PlayMOBY tarball; in fact it's the directory where is "pmb_configure.pl" script
The script pmb_configure.pl also gernerates a setenv (.setenv) file containing two environment variables: PMBBIN and PMBCFG
To use these environment variables, type the following command each time you connect to your PlayMOBY environment
First of all, a little word on how we consider webservices: for us, it is just a script/executable embedding.
That's why our webservices are based on a system call of a standalone script handling infiles and outfiles.
By this way, we can continue to use these programs using command line call, or embed these into programming pipeline or CGIs.
Deploying a BioMoby webservice using PlayMOBY environment is a 3 steps protocol:
We based our protocol onto the Mobyle XML format to describe our programs.
To generate Mobyle-xml files we developped a perl Module called Appli.pm.
It's based on a description of inputs, outputs and parameters using perl hashes.
Here's a sample code (ParamParser.pm module is also a LIPM perl module provided within PlayMOBY tarball):
The Mobyle XML file produced when the program is executed with --mobyle swith is:
Nevertheless, you can use whatever you want to produce a valid Mobyle-xml file.
This step will produce a standalone tarball: we analyse the Mobyle-xml to generate a Webservice configuration file.
N.B: We use such a configuration file to be independant of Mobyle DTD modification: if the Mobyle file change, we just have to modify our Mobyle parser and not all the downstream programs (using our configuration file).
This step leads to the creation of tarball containing the configuration file but also data to test the webservice and a log file.
To produce this tarball, please use the "pmb_MobyleParser.pl" script:
The following parameters are optional (but if you do not defined them, the system will ask for)
--tmp_dir=<temporary directory> this directory should be apache writable (/tmp is okay) --service_contact=<werbservice support email> --bin_fullpath=<full path to the binary/script embedded in the webservice> this parameter is already defined in the Mobyle-xml file, but we redefine it here because you could imagine to generate the Mobyle file on a serverA and then deploy your webservice on serverB; in this case, there is a chance that the executable is not in the same path. --async whether or not to deploy your web-service as an asynchronous one (Perl module WSFR::Lite is mandatory)
Then the program will ask you for test data for each input. You just have to give raw data an PlayMOBY will convert it into BioMoby XML format.
Once the tarball is generated, you have to go into PlayMOBY/services directory.
First of all you have to make a directory where you will store your webservices.
A good practice is to create a directory by service type: for example you can create a proteic directory to store your proteic analyses webservices and a nucleic directory to store your services dealing with nucleic sequences.
Another good practice is to create a directory by user in the case of a multi-user project.
Then untar your webservice tarball in this new directory.
The final step is to register and test your webservice. You have to choose in which registry you want to register your service.
A good practice is to first register it in the opencentral registry which is a test one. Once all the tests passed, you can deregister your service from opencentral and register it in the public production one called mobycentral.
To register, deregister and test your webservice, please use the "pmb_DeployWS.pl" script:
The mandatory parameters are : --services=<service name> this can be the service directory or the service configuration file "myWebService.cfg" located in the service directory; You can provide a list of services (separator = space) Example: /www/www-bioinfo/biomoby/playmoby/services/WelcomeProgram --central=<central name> this is the central name where the service is/will be registered; By default the public central (mobycentral) is used but we provide also the official test registry information (opencentral) --register : this switch will call the register procedure leading to the registration into the central and the production of a rdf file or/and --deregister : this switch will call the deregister procedure (empty the rdf file, then call the Rdf-Agent) or/and --test : this switch will call the test procedure, i.e. execute the webservice with the test data you provided during step II if you want to use special parameters for your webservice (secondary articles), you have to create a file called parameters into the myWebService/test directory; the syntax of this file is parameter_name1=value1 parameter_name2=value2 ... or --all : consist in a sequential call of deregister + register + test or --pm : only produce the myWebService.pm file
This script will first generate the perl module corresponding to your webservice (myWebService.pm).
This module contains few subroutines among which is myWebService, the effective function called by the dispatcher.
The test procedure will execute your webservice; then log messages are written in the myWebservice/log file.
If you want to stop logging your services, just create a log.stop file in your webservice directory (touch myWebservice/log.stop) .
To monitor the availability and stability of your webservices, you can use the program pmb_CheckWS.pl within a cron.
This program checks:
There are two ways to test the webservice answer produced with the test inputs (and parameters):
To use this script :
--ws_dir=<directory> directory where are located webservices --central=<central name> this is the central name where the service is/will be registered; By default the public central (mobycentral) is used but we provide also the official test registry information (opencentral) --nomail : this switch makes the program only produce xml report without sending any mail (EXCEPT FOR ERRONEOUS SERVICES) If this switch is not specified, all service developpers will receive an email foreach one of the services they deployed. Nevertheless, the PlayMOBY administrator (see PlayMOBY/cfg/CheckWS.cfg) will receive an email with the URL of the global report. --bioworkflow : to generate BioWorkFlow consortium report
This script produces 3 XML reports.
PlayMOBY is mainly written in perl and use some linux binaries.
NB: We distribute some of them within PlayMOBY archive for strong dependancies reasons (compatibility of releases).
Moreover we distribute perl Modules developped by our team at LIPM:
Here is a list of sample scripts that can be deployed as web services
PrintHello This program takes a list of nicknames as input and print a welcome sentence foreach one.
PrintHello_secure This program takes a list of nicknames as input and print a welcome sentence foreach one.It uses perl module Auth.pm to identify the user if provided, and modify output in consequence.
PrintHello_Async This program takes a list of nicknames as input, sleeps 60 seconds and prints a welcome sentence foreach one.
msf2fasta Converts Msf file into a Fasta file
msf2phylip Converts Msf file into a a Phylip interleaved file
tab2fasta Converts tabulated file into a Fasta file
compare_list Compares two lists of words
blastp_swissprot Blastp against Swiss-Prot database sample
a_simple_blastp Blastp against Swiss-Prot or Enzyme database sample
fastaCollection2multifasta Merge of a list of fasta files into one (UseCase to deal with input collection)
multifasta2fastaCollection Split of a multi-fasta file into a list of single fasta sequence files (UseCase to deal with output collection)
Main contributors are members of the LIPM Bioinformatics team:
For bug report, information request, please contact Sebastien Carrere