OSCG:Tutorial
From Vd
This is a brief description of the use of the Bioportal at University of Oslo (www.bioportal.uio.no). It details certain steps necessary to complete registration, uploading files, editing files, running applications and managing jobs.
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Registration
This section is not relevant to users from Norwegian Universities or Høgskoler that are part of the Feide collaboration. They only have to log in using their Univesity/Høgskole username/password in the Feide login portal Moria. If you are wondering whether you have a Feide ID, please check out the Feide homepage (http://feide.no/).
Start the registration on the registration page. Fill in the necessary details. Your account will be set up by the Bioportal administrators and verified to your registered email address. NOTE: all registrations must have an academic affiliation and therefore academic email address. This is due to software licences. If you want/need access to restricted applications, please let us know at the same time which applications and why you should have access (license, collaborations, ...). The status of the applications can be found in the applications application information page. This page also describes briefly the implementation of the applications on the portal. If you want other applications than what is already installed, please fill in the name and appropriate URL.
Logging In
Feide users may log in at any time on the Feide login portal Moria. All other users need to recieve a confirmation that their account has been activated. This is done in the usual manner on the login page, by providing the username and password (the same as suggested in the registration).
Projects
A recent addition to the Bioportal is the ability to organize your files and jobs in projects. Every file belongs to a single project, and a job can only use files from a single project. Projects can be listed, created, and deleted in the Projects section. Note that it is not possible to delete a project until all its files and jobs are deleted.
To create a new project, enter its name in the Title field, and click Create. Note that only ASCII letters (a-z, A-Z), digits, '.', '-', and '_' are accepted in the title. Any other characters are removed.
The default project for new users is my_project, and if you do not want to use the project functionality, you can simply let all files and jobs belong to that project.
Uploading Files
The first thing you want to do when starting an analysis on the Bioportal is to upload your input files. This is done in the Upload new files to the system box, which is located in the left side menu after you have logged in. After locating the file on your computer (either by browsing or typing the full path), you select which project the file should belong to by using the pull-down menu, and upload the file with the Add file button. The new file will then appear in the File Admin section. This section may also be used to manage your files (delete, edit, view, move to another project, ...). Two uploaded files may have the same name.
Note the expiration date on the files! Please keep a local backup of your files, so you don't lose any files or results.
Viewing and Managing Your Files
Once you have uploaded files, you can list your files in the File admin section. Certain attributes of these files are listed also. Note that you may have two files with the same name, and that files expire (are deleted) after a while.
Using the order files by menu on the bottom, you may sort your files after different criteria. One can also download, delete or view files, by checking the select box (just before the Edit link) for the selected files, and press the appropriate buttons at the bottom of the page. To move the selected files to a different project, choose the desired project in the drop menu and press Move to project:. Using the Edit link to the right of a file, you may edit ASCII files in a simple editor on the Bioportal.
Submitting Jobs
You start a new job on Bioportalen in the Submit job section.
First you choose which project to select input files from in the pull-down menu at the top. Then you select input files by checking the select box in the file list. (If the application needs to know which file to use as control file, etc., you get the opportunity to specify that later.)
You then select the application to run, and which resource to run it on, by choosing the appropriate application@resource in the Application pull-down menu. To shorten the list, you can limit the choices by selecting an application category and/or resource in the pull-down menus to the left.
Finally, choose a name for the job (optional), and click Submit to continue. You are then transported to the appropriate application page. The appearance of this page will vary between applications, however it should hopefully be self explanatory together with the program documentation found in the Applications top menu section. In general, when appropriate options are chosen, click the Start Computation button on this page to start the application.
Presently the user can choose between 3 different queue options when submitting an analysis on the Bioportal, however each queue works in a different manner and this should be considered when submitting analyses.
Bioportal Queue: For most applications this is the "default" queue option, it is stable and Bioportal specific. It is recommended for large time consuming or multi-CPU analyses. As it is the "default" the queue length may also be longest.
Bioportal "low priority" Queue: This has a high number of available CPUs and waiting times are low, however the Bioportal has "low priority" here. This means that if a prioritized "non-bioportal" analysis is submitted it could use all available CPUs and therefore throw-out (and stop) your analysis. This queue is recommended for small jobs with short run-times. You submit jobs in this queue at your own risk!
UiO Queue: Again a queue with a high number of available CPUs and lower queue times, however these CPUs are accessible for all UiO users and are not Bioportal specific. This means that there can be huge variations in use. This, like the Bioportal queue is stable and once your analysis starts it will not be thrown-out, however it may be "paused" while higher priority jobs use CPUs. This queue is recommended for large time consuming or multi-CPU analyses.
Managing Your Jobs
The status of your jobs can be viewed in the the Job admin section. Here all of your jobs are listed along with some properties.
These properties include submission date, resource submitted to, and status (local/remote) of the job. The local status has five possibilities:
- Submitted -> Job waiting to be submitted to the resource.
- On resource -> Job submitted to resource
- Cleaning -> Job is finished, and filecopy and cleanup is underway.
- Postproc -> Job is beeing postprocessed (plotting, etc.)
- Completed -> The job is finished and output returned.
The remote status has three values (if any):
- Waiting -> Job is waiting in the queue to run.
- Running -> Job is running on resource.
- Finished -> Job is finished.
In this directory you may also apply certain actions to your job. This is done by selecting the appropriate job and pressing the button for the desired action:
- Download: Download the job files as a zip-file
- Stop: Stop the job
- Delete: Delete the job
- View: View the job files (see below)
Note that deleting a job will not affect files in the File admin section.
Viewing a Job
When the job is finished you may see the output from your job by selecting a job and pressing View in the Job admin section. Here all files belonging to one job (input/output) are stored. This section also contains the output of any postprocessing results (plots etc.) from your job.
You can take several actions, by selecting one or more files and pressing the appropriate button:
- View: View the file(s)
- Copy Home: Copy the file(s) to the File admin area
- Download: Download the file(s) as a zip-file
- Resubmit Job: Resubmit the job
- Copy Job & Resubmit: Make a copy of the job and resubmit that job
Note that your output files will be written over when using resubmit. If you want to keep the old output files, use Copy job & Resubmit.