BioCloud
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2.Application Management

2.1 Application List

This page will show all the created applications and the shared applications from other persons of the current login user. User can edit,delete the application and share,publish applications to other persons.User click the “Add” button will open the web page of create one application and “Load Xml” will open the upload page of create one application.Note: If the edit operation has been done,user need to wait the application to be validated by BioCloud. If the application has been published,user can not delete it any more.

 Share an application:Users can share the application to other person,when the user login into the system the shared application can be used.The shared application only available for the shared users.

 Publish an application:Users can publish the application immediately or publish at the given date.Click the “Browse” button, the application type dictionary will be loaded.When the application published, all the BioCloud users can use this application.

2.2 Create an application

Two ways are available to create an application in biocloud, one is the web form,the other is xml format.

1)By web form

When click “Add” under application list ,the page for create application will be show.All the items under this page are described here.

Description of the parameters as following table.
NameDescription
Namean unique application name,which consisted by letters(a-z,A-Z),numbers(0-9) and underline(_),such as add_number. Note:white space and other special letters are not allowed.
Descriptiona brief description about this application
Main script a script used to active this application.The users need to provide the script running method except the detail path.
                     Such as java -jar drawpic.jar
                     perl drawpic.pl
                     drawpic.sh
Command parameters a read only field, used to show the input and output parameters which configured by users
Reference paperseveral publish papers which used by this application
Script file all the scripts used by this application.If the script file more than one file,users should packaged all of them into one file.If the script used some public softwares, users can describe them in the document file.
Document file the document describe how to deploy this application under linux machine.If some system environment parameters need to configure,users must describe clearly here
Test data file: the minimum test data used to test the application.
Emailan email address used to contact the person if we deploy the application encounter some problems
Submit method two method provides, single task for applications which run on single machine;multiple tasks for applications which run under MPI environment. Biocloud use PBS to schedule task, users can set the node number,cpu number, running queue,running memory and running time.
Helphow to use this application.We suggest users provides information as detailed as possible.

Set input parameters

For most command line, users can use command parameter and the default value to finish.

Description of the parameters as following table.
NameDescription
Namean unique parameter name in this application,which consisted by letters(a-z,A-Z),numbers(0-9) and underline(_),such as add_number. Note:white space and other special letters are not allowed.
Value type the value type of this parameter,different value type will have different item type.
Command paramthe command line prompt parameter, which mostly used in perl script,such as -i
Item labela short label about this parameter.
Item typeHTML item used by this parameter
Default item value a default value of this parameter,which will show by the chosen item type.
Item description a brief description about this parameter
Show in submit pageif checked, it means this parameter will show in the submit page by the chosen item type.
Allow white spaceif checked,it means allows white space between command parameter(-i) and the parameter(i1),such -i i1

Set output parameters


Description of the parameters as following table.
NameDescription
Name an unique parameter name in this application,which consisted by letters(a-z,A-Z),numbers(0-9) and underline(_),such as add_number. Note:white space and other special letters are not allowed.
Command param the command line prompt parameter, which mostly used in perl script,such as -o
Item label a short label about this parameter.
Item typeHTML item used by this parameter,only two types support textbox and checkbox
Default item value a default value of this parameter,which will show by the chosen item type.
Item description a brief description about this parameter
Show in submit pageif checked, it means this parameter will show in the submit page by the chosen item type.
Show in result page if checked,it means this parameter will show in the result page when the task finish
Allow white spaceif checked,it means allows white space between command parameter(-o) and the parameter(o1),such -o o1

Param Order

When user click the “Param Order” button, the web page of adjust the order of command line parameters will be opened. Click the “Up” or “Down” the button to active it.

2)By XML format
BioCloud supports use XML format to load application.User can click “Xml Configuration Template” to view the template xml file.

2.3 Application share list

This page will show all the shared applications of current user. The user can cancer the share application.

2.4 Application publish list

This page will show all the published applications of current user.When the application has been published, it can not be canceled.

©BIG 2010, Beijing Institute of Genomics,Chinese Academy of Sciences No.7 Beitucheng West Road,
Chaoyang District, Beijing 100029, PR China