Emboss

Description
	EMBOSS is a suite of bioinformatics applications i.e. sequence analysis programs and other assorted programs like enzyme kinetics.
Site	Version (Latest: v6.3.1)	Notes
ngs.rl.ac.uk	v4.1.0

License

Emboss is Open Source Software.

Running Emboss on the NGS

Some infrequently used Emboss utilities may not be working at all sites. If you find one that you need that doesnt work please let the NGS helpdesk know.

• Databases

  The available applications can be found here, while for information about the available databases refer to the Bioinformatics, applications and databases page.

  Access is provided to full sequence entries and annotation searches using SRS indices of embl , uniprot , swissport , trembl and genbank . If you need any further configuration , please contact the NGS helpdesk.

  Alternatively, you could create your own .embossrc file. This may require setting the EMBOSS_PROXY to the site http proxy. For example at RAL include in your .embossrc file the line:

  set EMBOSS_PROXY "wwwcache.rl.ac.uk:8080"
  

  and set your EMBOSSRC environment variable to point to the location of your .embossrc file.

  The example input files shown below can be found at

  gsiftp://ngs.rl.ac.uk:2811/apps/emboss/examples/seqret rel_tpa_inv_01_r90.dat

• Submission Using the UI/WMS

  To submit an Embos job via the WMS, login to the UI and create a JDL file as below, replacing your ngs ID on the UI for ngsxxxx, then submit using the example JDL below. This file specifies that output files will be automatically returned to your input directory on the UI when the jobs completes. You do not need to manually retreive them using the job-output command. Submit this job using:

  glite-wms-job-submit -o jobIDs -a emboss.jdl

  Type = "Job";
  JobType = "normal";
  Executable = "/usr/ngs/EMBOSS";
  Arguments = "seqret rel_tpa_inv_01_r90.dat seqr.out -osformat fasta";
  StdOutput = "std.out";
  StdError = "std.err";
  Myproxyserver= "myproxy.ngs.ac.uk";
  InputSandbox = {"rel_tpa_inv_01_r90.dat"};
  InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/emboss";
  OutputSandbox = {"std.err","std.out","seqr.out"};
  OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/emboss";
  Requirements = (
       member("NGS-UEE-EMBOSS", other.GlueHostApplicationSoftwareRunTimeEnvironment)
  );
  #Rank = other.GlueCEStateFreeCPUs;
  ShallowRetryCount = -1;

• NGS Web Portal Submission

  After logging in to the NGS portal, select the "Emboss" template under the " Bioinformatics" category and make the amendments appropriate for your specific job. Read the description page of the template for further details.

• Submission Using Globus

  In what follows we will show some example-run of EMBOSS applications.

  The string 'xxx' in the subsequent commands is to be replaced with your local id on NGS.

  You can also create a working directory to run the job by adding, for example, "(directory=/home/ngsxxx/emboss)" to the string in quotes below.

  • Example-run of seqret on ngs.rl.ac.uk

    To submit a seqret job use the following command (one line. You should not include the backslashes), after replacing the pathname of the input file and arguments with the ones of your choice:

    globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf \ '&(stderr=seqr.err) \
    (executable=/usr/ngs/EMBOSS) \
    (arguments=seqret rel_tpa_inv_01_r90.dat seqr.out -osformat fasta) \
    (jobtype=single)'

    • The above job transforms a flat text file to fasta format.
    • The input file for this job is rel_tpa_inv_01_r90.dat
    • This runs the default version. To run 4.1.0 specifically use EMBOSS_4_1_0 instead of EMBOSS.
    • To run at a site, other than ngs.rl.ac.uk, change the string "ngs.rl.ac.uk/jobmanager-lsf" to that for the relevant site.
    • If you are using a custom .embossrc file add in the globusrun command the following "(environment=(EMBOSSRC /home/ngsxxx/))" where EMBOSSRC denotes the path to the directory you have saved your .embossrc file.

     

  • Example-run of wossname on ngs.rl.ac.uk

    TThe following example shows how one can use more interactive tools like wossname through globus. wossname is used to find EMBOSS programmes by looking for a keyword you submit as an argument, as in the following example (one line. You should not include the backslashes):

    globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf \
    '&(directory=/home/ngsxxx/emboss)(stdout=woss.out) \

Further Information

• Online Reference Manual for EMBOSS
• EMBOSS Home Page
• EMBOSS User Mailing List

The NGS cannot offer scientific support for this application. However if you require further information or believe there is something wrong with the installation, please contact the NGS support centre.