mobyle 1.5 - mobyle workshop - september 28, 2012

Mobyle 1.528 septembre 2012, Institut Pasteur

What is Mobyle

What's new in Mobyle 1.5

● Workspace management● Multiple data● Tutorials● BMID● BMPS● Availability

Advanced workspace management

● it becomes hard to navigate and manage user data and jobs:○ jobs have generic names: service name + date○ data sometimes have generic names: parameter name

or file name○ regular users can have large numbers of jobs and data

stored in their workspace

● solution: provide a way for users to easily rename their important jobs/data or remove the ones which are useless

Advanced workspace management

Bookmark as "x"Generic job/ bookmark

names

Advanced workspace management

Rename jobs(click on the pen icon)

Remove or sort jobs / data bookmarks in the overview panel

Advanced workspace management

Rename jobs

Advanced workspace management

Job is renamed

Advanced workspace management

jobs/data bookmarks can also be renamed in the Overview panels

"Multiple" data

● Sometimes a program accepts a list of n files as input

● In Mobyle 1.0.x, it is not possible to specify this behaviour

● The workaround is to create web interfaces with a fixed but limited number of parameters which will be translated into files

● not flexible enough!

"Multiple" data

Three databoxes let you specify three files at most as program input

"Multiple" data

You can add new databoxes "on the fly" with the [+] button

You can remove them with the "remove" button

"Multiple" data

Two files have been used as input for the same parameter

The order of the inputs is preserved through the order on the command line

"Multiple" data

Process the value using the separator and the command line formatting code in <format>

You specify a "multiple" type by merely adding the "Multiple" prefix to the datatype

Tutorials

● Tutorials in Mobyle 1.0.x are hard-coded: a limited list of HTML pages

● Depending on the context of each server, one might want to add/remove such pages:○ to provide help pages about a given service○ to explain a given use-case

● This requires the modification of Mobyle code (portal templates) which is overwritten on each update and may even break it altogether.

● not flexible enough!

Tutorials

Tutorials are HTML web pages which can now be deployed the same way

as others Tutorials can be added, classified and searched the same way as the other

"services"

Tutorials

A tutorial is a service XML consisting mostly of an <interface> tag that contains the

displayed HTML

Locally stored dependencies can be stored in a local directory that has the same name

as the XML file, minus its extension(just like viewers/widgets)

Visualization/Edition Widgets

Edition and chaining

Export snapshots

$apt-get install mobyle

Availability

http://bit.ly/PTG0N7

http://bit.ly/NyVaUl

Mobyle 1.5, September 2012

● Edition widgets: Mobyle 1.0.5+, May 2012● BMID● BMPS

Roadmap

Mobyle distribution

from 1.5 version Mobyle exists in two flavors:

● Mobyle+BCBB-1.xx.tar.gz . With BMID (programs editor) and BMPS (user graphical workflows)

● Mobyle-1.xx.tar.gz . Without BMID (programs editor) and BMPS

(user graphical workflows)

Acknowledgements

NIAID: BMID and BMPS developmentNick WeberRamandeep KaurJanet HeJennifer Dommer

GenOuest: packaging effort and more...Olivier Sallou