On Quarry, what are EMBOSS and wEMBOSS, and how can I use them?

On this page:

Introduction

EMBOSS is open source software for molecular biology analysis. With this software you can perform sequence alignment (local and global), automatically transform different data formats, get retrieval sequences from your local computer or database or the web, find motifs and enzyme sites, and use drawing tools. wEMBOSS is a web interface to most EMBOSS programs.

The software is available to Indiana University students, faculty, and staff. This document provides information about accessing EMBOSS on the Quarry cluster and wEMBOSS on the Discern server. It is not intended as a general guide to using EMBOSS and wEMBOSS or to particular analyses.

EMBOSS and wEMBOSS at IU

The software is available through both the web interface and the command line. If you plan to use EMBOSS or wEMBOSS, note the following:

  • EMBOSS is installed on the Quarry cluster.
  • The wEMBOSS web interface is installed on the Discern server (discern.uits.iu.edu), and is suitable for most people who prefer to access EMBOSS from a Windows computer. Each user has a 100MB home directory. All files will be kept on the Discern server and will be available when you log in again. Files generated by wEMBOSS and older than 180 days will be automatically removed to free up space.
  • If you have large jobs, use EMBOSS on Quarry via the Unix command line and the shared scratch space (/N/gpfs). Files in the shared scratch space that are more than 90 days old will be automatically deleted to free up space there.
  • All users are responsible for reading the Quarry usage policies.
  • EMBOSS and wEMBOSS databases are updated bimonthly.

Requesting accounts

To apply for an account to use EMBOSS and/or wEMBOSS on Quarry, visit the Account Management Service at: https://itaccounts.iu.edu/

After you log in (using your Network ID), click create more accounts. Follow the instructions to create your Quarry account. You will receive notification via email when your account is ready to use.

To use wEMBOSS, you must also email High Performance Systems to request an account on Discern and specify that you want to use wEMBOSS.

Using wEMBOSS

Features

  • Each user has private space to organize and store data.
  • You can easily organize your work in projects and subprojects.
  • Functions are listed in alphabetical order or classified in groups.
  • The manual is available on the program page.
  • Multiple options are available for the data format and file format.
  • You can view results instantly as a web page or save them in a file.
  • You can download results to your workstation.

Accessing and using wEMBOSS

  1. Go to: https://discern.uits.iu.edu/wEMBOSS/
  2. Log in with your valid IU Network ID.

  3. To start a new project, click New project at the top of the project management page and give the project a name. The project here is similar to a file folder you might use to organize your papers. For example, say you have two projects ongoing, one about the mutation of mitochondria and the other about the recombination rate of mitochondria. You can either create two projects, "mutation" and "recombination", or put them in one project "mitochondria" and have subprojects "mutation" and "recombination" within that one project.

  4. On the project management page, choose a program by its function or from the alphabetical list on the left. The program page will replace the project management page, but the command list on the left side will remain, so that you can easily switch to other functions.

  5. Upload your data and set up options if necessary, and then click the Run button on the program page to run the program. The result will be displayed in a new window.

  6. You can save your results on your local computer if you wish. All files generated are kept on the Discern server and will still be available when you log in again. Files generated by wEMBOSS that are older than 180 days will be automatically removed to free up space.

To see the manual, click the Manual button at the upper right. A new window will open to show you the manual.

Using EMBOSS

Features

  • Use EMBOSS from the Unix command line.
  • EMBOSS is appropriate for use from scripts.
  • Use TORQUE for large tasks.

Accessing and using EMBOSS at the command line

You can use EMBOSS at the command line after you receive email confirming that your Quarry account has been set up. To access EMBOSS, use an SSH client to go to quarry.teragrid.iu.edu. Use your IU Network ID to log in.

Note: SSH Secure Shell Client for Windows is no longer available for download from IUware or the SSH Communications Security web site. For alternative SSH and SFTP clients, see At IU, what SSH/SFTP clients are supported and where can I get them?

In Mac OS X, you can use SSH from the Terminal. In the Finder, from the Go menu, select Applications, then Utilities, and then Terminal. Enter ssh -X username@quarry.teragrid.iu.edu . Replace username with your username.

After you have logged in, add a softkey to reach EMBOSS by entering the following command:

soft add +EMBOSS

To see all available commands in the EMBOSS package, enter wossname .

For help with EMBOSS, see the online documentation.

If your job will take more than 20 minutes to run, you must use TORQUE (also called PBS) and the serialjobscript. For help, see What is TORQUE/PBS? Note that TORQUE doesn't support interactive mode.

If you have questions