Changes between versions


  • NEW: allow to display results files located inside a subdirectory.
  • NEW: allow to add a whole directory in zip results.
  • bug fix: the queue was not set properly when some nativespecification are provided.
  1. Portal
    • bug fix: do not display default interface if custom interface is defined.
    • bug fix: correct the generated html for custom interfaces in job results page.


  1. Portal
    • fix bug preventing results from loading when a running job finishes (#1928)
    • fix bug where a job results page sometimes displays twice the resultbox (#1764)
  2. Utilities
    • NEW mob_stat: script that provides basic statistics about portal usage
    • NEW mob_log_rotate: script to rotate and compress Mobyle logs


  1. fix issue (#2044)
    • When program parameters have example data but no comment, the [use example data] button does not work.
  2. fix issue (#2022)
    • Error when submitting workflows that run tasks with multiple inputs
  3. fix issue (#1926)
    • the status of the jobs with a retun code != 0 are never updated so they are stuck in submitted, pending, running, ...
  4. fix issue (#1761)
    • inline help is not displayed when coded in HTML
  5. add User-set per-job email notification for job completion (#1744)
    • Users should be able to specify on a per-job basis if they want to get an email job completion notification.
      only show the control if dont_email_results is not set to true and if the user email is defined.


  1. New converters for Alignment formats
    • We provide a set of new converters to convert alignments in fasta, nexus, phylip, stockholm in phylip-relaxed format.
      phylip-relaxed is the format used by Phyml and morePhyml. These converters needs biopython to perform the conversion
      so you NEED to install biopython if you want to use them (It's not need to install numpy or reportlab for these functionalities).
      The converters will automatically be installed with the Mobyle installation/upgrade, but to activate them you must
      add them in DATA_CONVERTER in the Mobyle configuration, like this:
        DATA_CONVERTER = {
                 'Sequence': [ squizz_sequence('/usr/bin/squizz') ],
                 'Alignment': [ 

      To take full advantage of these new converters, you also need to update your program definitions (>=5.1.1).
  2. BMPS
    • Workflow description update fixed (#1636)
    • Default values sometimes not displayed in form task panels fixed (#1762)
  3. Portal
    • Tutorial images fixed in debian package-like configurations (#1631)
    • Example data can now also contain XML (#1640)
    • Portal freeze upon loading fixed (#1647)
    • accents supported in job names (#1673)
    • renamed jobs correctly sorted (#1674)
    • Font size for workflows is now ok (#1709)
    • "Tutorials" and "My Workflows" menus can be customized again (#1737)
    • Portal freeze when closing widget window after bookmarking fixed (#1739)
    • Forms displaying sometimes when refreshing the portal fixed (#1757)
    • Parameter values unmodifiable after loading from history fixed (#1758)
  4. Execution server
    • BMPS job error fixed (#1742)
  5. Documentation
    • chaining rules description updated (#1675)


  1. BMPS: BCBB Mobyle Pipeline System is a graphic interface which lets users create their own workflows, which can be launched directly
    from the BMPS interface but also from the Mobyle portal.
  2. Portal
    • bookmarks and jobs can now be renamed in left menus (#1162)
    • tutorials are now customizable. please note that to keep previous tutorials you have to download and deploy the pasteur-tutorials
      package (#1165).
    • the values chosen in Choice and MultipleChoice controls are now displayed in the "job inputs" panel using their label instead of
      their "command-line value" (#1220).
    • services now support multiple-file inputs.
  3. Execution server
    • Job submissions control configuration: !! MAX_SIMILAR_JOB_PER_USER replaces SIMULTANEOUS_JOBS !!
      MAX_SIMILAR_JOB_PER_USER represent 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.
    • support for module is now included (


  1. Portal

    *bugfix: Foreign jobs opened in the Mobyle portal freeze the interface (#1182)
    *bugfix: Program import blocked because of an irrelevant XSL transformation (#1224)
    *bugfix: Interactive pipes broken in Mobyle (#1227)
    *bugfix: job submission fails silently in case of error (#1232)

  2. Execution server

    *bugfix: Help request emails sent only to the first recipient if multiple recipients are specified (#1123)


  1. Portal
    • bugfix: "further analysis" button not working from data bookmarks (#1155).
    • bugfix: simple bookmark click induces chaining if a service is selected in "further analysis" (#1159)
    • bugfix: recurring problem in AJAX workspace update (#1156)
    • bugfix: advanced options button is not displayed when all the parameters are "issimple" (#1175)
  2. Admin tools
    • it is no longer possible to publish services with mandatory parameters and no vdef as advanced parameters (i.e. not "issimple") (#1166).
  3. Execution server
    • bugfix in DRMAA error handling (r4157-r4158).


  1. Portal
    • possibility to display only "simple" parameters by default, and toggle between simple and advanced forms. "Modified"
      parameter values are also outlined in the portal (#1064).
    • data edited in "viewers" can now also be reused directly (piped/bookmarked) in the portal (beta/hidden feature since r3610)
    • viewers custom code now also supports more flexible custom operations (#859)
    • it is now possible to specify a progress report file: the contents of this file are now displayed and updated even during
      its execution (#867)
    • several minor bugs fixed: jumps in the portal upon history refresh (#1070), no error message sent when the user workspace
      is full (#1065), pipe problems (#932), job outputs interface customization (#929), documentation links (#1078)
  2. Execution server
    • the configuration of the acceptance or refusal of jobs based on the number of similar jobs is now completely configurable
    • the handling and reporting of drmaa errors has been improved (#1076)
    • logs do not disappear partially anymore when they are rotated (#1075)
  3. Admin tool fixes
    • custom messages can be specified when blacklisting a user per IP or email (#1123)
    • updating does not overwrite your CustomClasses! (#1136)
    • mobclean does not crash when processing "dirty" job folders (#857)
    • mobdeploy minor fix (#835)
  4. Documentation
    • interface customization documentation improved (#921)
    • portal header and footer documentation corrected (#800)


  1. Portal:
    • improved workflow display (#745 , #747 , #753)
    • nested workflow jobs do not display in a new tab (#751)
  2. Execution server:
    • Mobyle allows multiple job executions if they are subtasks of the same workflow (#738)
    • allow a workflow to execute a workflow as a subtask (#734)
  3. Admin tool fixes:
    • mobvalid and mobdeploy apply new rules for parameter name.
      from now on, some words are forbidden as parameter names (because they can create conflicts in the resulting HTML DOM) (#683 , #708).
    • mobjobw displays workflows as other jobs (#742)
    • mobyle can deploy several imported services in one time (#756)


  1. A few bugfixes in the portal interface:
    • user parameter and error messages are sent with user help requests (#699,
      broken in prior 1.x releases).
    • double submissions caused by a defective waiting screen fixed (#682)
    • broken MobLinks functionality is back (#725).
    • portal static document links are now versioned, allowing to bypass browser
      cache mechanisms upon portal update (#681).
    • users can simultaneously log-in from multiple browsers (#680)
  2. Execution server:
    • workflow status is updated on each subtask status update (#686).
    • workflow status updates are now performed less frequently (#693).
    • user error messages now explicitely mention the expected datatype (#709).
    • user parameter values can now only be ascii-compatible (#727).
    • job status is properly set even if the DRM is unreachable (#728).
  3. Admin tool fixes:
    • mobclean now does not fail if the '.htaccess' file exists (#703),
      checks that no other instance of itself is running prior to launch (#710),
      and uses a lot less memory to run (r3931, r3932, r3933).
  4. HTTP API fix:
    • job simulation can be used (#723, but still needs to behave correctly with files #724)


  1. Mobyle does not require the PyCaptcha anymore (r3864,r3865,r3870)
  2. A few bugfixes in the Execution server:
    • job emails are now always sent if configuration specifies it (#679).
    • workflow execution engine does not fail if linking two parameters between the same tasks(#649),
      and handles correctly no-output style workflows (r3853).
    • workflow jobs now seamlessly handle the removal of remote jobs (#640).
  3. A few bugfixes in the portal interface:
    • comments can be expanded in the standalone job result pages (#673)
      (warning: this requires that you redeploy your services, and existing jobs won't be fixed).
    • freezed screens after job submission (#669).
    • paragraph comments do not appear automatically upon paragraph "maximizing" (#666).
    • modal dialogs (e.g. captcha problem) do not remain on screen after validation (#647).
    • input fields such as captcha answer now automatically have the focus, even on old (e.g.,FF3.5)
      browsers (#571).
  4. Admin tool fixes:
    • mobclean does not complain anymore about any .htaccess file in the jobs directory (#667).
    • mobdeploy does not deploy anymore invalid service descriptions (#589).
  5. API improvement:
    • it is now possible to get a service description using JobFacade.parseService() instead of
      JobFacade.create() (#583).


  1. minor features:
    • portal customization improvement (#585): the header and footer of the portal
      can now be customized, check the configuration guide for more details.
    • a download button is now directly available for data bookmarks (#596).
  2. multiple bugfixes in the portal interface:
    • the jobs tab removal checkboxes now work properly (#573).
    • the simple parameters can now be modified after a refused submission fails (#574).
    • job results and workspace data can now be directly piped to workflows (#581).
    • jobs can now be accessed from another session to facilitate sharing and maintenance (#588, #625).
    • interface is more informative about workspace refreshes and other actions (#592,#593).
    • multiple workflow execution problems (#594, #605, #606, #608, #624).
    • multiple workflow diagram browser compatibility issues fixed (#292, #567).


  1. Viewers: viewers offer the possibility to visualize data in the Mobyle portal
    using web-compatible components, to provide a more readable representation.
    For instance, multiple alignments can be visualized with Jalview, Protein 3D
    structures can be visualized with JMol, RNA Secondary structures with VARNA, or
    phylogenetic trees with Archaeopteryx.
  2. Workflows (beta): Mobyle services chainings can now be automated by providing
    predefined workflows.
  3. Many portal improvements, including the possibility to customize your welcome page
    and user workspace management interfaces that facilitate the visualization and cleanup
    of user jobs and data.
  4. A new plugin-like architecture for the converter modules: you can associate
    to each data type and format a validator/converter module, that will detect,
    validate and convert the format of user data when appropriate.
  5. The execution system has been rewritten to be highly flexible:
    Mobyle now supports new DRMs, including LSF (via the DRMAA API). It is also
    possible to manage multiple execution configurations, allowing for instance
    to send jobs to different DRMs based on your needs.
  6. OpenID support: you can now configure Mobyle to let users authenticate themselves
    using OpenID, in order for them to avoid the management of a new Mobyle-specific
  7. Google Analytics support: you can configure Mobyle to track users
    activity with a Google Analytics account.


  1. fix small bugs.
  • in MultipleChoice value was not parsed correctly.
  • allows the job to make a subdirectory in the job directory
  • in duplicate job submission prevention.
    (this method failed when lot of jobs from same program were submitted at same time).

From 0.97 to 0.97.1

  • fix small numerous bugs.


  1. Small numerous bugs were fixed.
  2. Mobyle is ready to use with python 2.6.
  3. Duplicate job submission (2 jobs with identical command lines and parameter values cannot run at the same time from the same user) is now prevented.
  4. Logging system has been improved.
  5. Job status management is improved to be more robust and consistent with respect to the different execution systems.
  6. There is a new plugin-like architecture for the execution modules.
  7. We now offer the possibility to create links to pre-loaded Mobyle forms from external pages: it allows web application developers to directly link their independent database or tools to Mobyle.
  8. An "advanced settings" option in the programs list allows to sort programs either by server or by category (servers mixed), which can be more appropriate if using the MobyleNet functionnality.
  9. Some administrative tools (mobclean & mobdeploy) have been improved.


  1. A completely automated setup procedure is now included, which tests for requirements and handles version upgrades "gracefully".
  2. Mobyle program definitions are now described using the Relax-NG language, which is far more powerfull and readable than the previous DTD. However, the format itself hasn't changed a lot and previous XML program definitions should be compatible.
  3. User workspaces are stored using XML instead of python pickle, which was unreadable for administration tasks and was too sensitive to source changes. Furthermore, they should be far more robust with respect to concurrent accesses.
  4. We now index program definitions to improve the portal performances (for instance, in Mobyle 0.9, programs list display was far too slow).
  5. Thanks to the use of Relax-NG, you can override form and job status normal displays to include custom HTML, which allows you to include for instance Java applets, flash, and just about anything that can be defined in HTML.
  6. Portal has been improved to load faster, handle better the "diversity" of browsers, and automatically refresh user workspaces (e.g., job status). Furthermore, css can be customized, using "local.css". Just check out the commented examples in this file.
  7. A set of useful administration tools has been placed in the Tools folder.
If you have a Mobyle 0.9 or 0.95 instance on your server, read the following points attentively because many things have changed since version 0.9 and even since 0.95:
  1. The files hierarchy has been cleaned up a bit, and some things(jobs, program definitions, user workspaces for instance) are not anymore where they used to be.
  2. A few additional requirements have been introduced, they are listed in the INSTALL file and should be tested for by the setup script.
  3. The deployment/indexing procedure (mobdeploy tool) HAS to be launched after the setup. ANY change to the contents of the program definitions should be followed by a mobdeploy.
  4. Given the amount of changes that has been accumulated since 0.9, we cannot provide a generic migration tool to convert 0.9 jobs and workspaces to 0.96. However, if you need to keep these data, we will be happy to help you, so please tell us.
  5. When you setup a 0.96, first try it on a test server, and make sure everything works ok.

Last update: Updated over 4 years ago