FASTA

License

The FASTA program and documentation may not be sold or incorporated into a commercial product, in whole or in part, without written consent of William R. Pearson and the University of Virginia.

Code in the smith_waterman_sse2.c and smith_waterman_sse2.h files is copyright (c) 2006 by Michael Farrar. This program may not be sold or incorporated into a commercial product, in whole or in part, without written consent of Michael Farrar.

Further details of the licensing conditions can be found from the Copyright file in the FASTA code download.

Users of this application should credit the code authors and the NGS accordingly and where applicable the specific site where the code is installed, when publishing work using NGS resources.

Running FASTA on the NGS

The example input files mentioned in the examples below can be found at:

gsiftp://ngs.rl.ac.uk:2811/apps/fasta/examples/humanDNA2.input

FASTA consists of a number of programs which are listed below:

• Serial programmes:

fasta34   fasts34  fasty34  ssearch34  
tfasts34  tfasty34 fastm34  fastx34  
tfasta34  tfastx34 prss34 

 

• Parallel programmes:

fasta34_t  fasts34_t  fasty34_t ssearch34_t   
tfasts34_t tfasty34_t fastm34_t fastx34_t 
tfasta34_t  tfastx34_t

 

• Submission Using the UI/WMS

  To submit an FASTA 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:

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

  Type = "Job";
  JobType = "Normal";
  Executable = "/usr/ngs/FASTA";
  Arguments = "fasta34 -H humanDNA2.input \"$DB_PATH\"/live/fasta_DB/em_rel_htc_hum 5";
  StdOutput = "fasta34-HTC.out";
  StdError = "std.err";
  InputSandbox = {"humanDNA2.input"};
  InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/fasta";
  OutputSandbox = {"std.err","fasta34-HTC.out"};
  OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngsxxxx/fasta";
  Requirements = {
      Member("NGS-UEE-FASTA", other.GlueHostApplicationSoftwareRunTimeEnvironment)
  };
  ShallowRetryCount = -1;
  

• NGS Web Portal Submission

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

• Serial Submission Using Globus

  Eg To submit a serial FASTA job on ngs.rl.ac.uk use the following command, replacing 'xxx' by your unix ID on the NGS site where the code will be run (one line. You should not include the backslashes):

  globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf \ '&(stdout=fasta34-HTC.out)(directory=/home/xxx/fasta) \ (executable=/usr/ngs/FASTA_34_26_5) \ (arguments=fasta34 -H humanDNA2.input \"$DB_PATH\"/live/fasta_DB/em_rel_htc_hum 5)'

  • This runs the default version. To explicitly run v34.26.5 use FASTA_34_26_5 instead of FASTA.
  • The input file is humanDNA2.input should be given as an argument not as stdin.
  • The FIRST argument should be the name of the FASTA program you want to use, that is fasta34 in this example.
  • The library being searched is the HTC library in FASTA format available in the /${DB}/EBI/output/fasta directory on the NGS site running the program. For information on the available EMBL Nucleotide Sequence data files in FASTA format see here

   

• Parallel Submission Using Globus

  Eg To submit a parallel FASTA job on ngs.rl.ac.uk use the following command, replacing 'xxx' by your unix ID on the NGS site where the code will be run (one line. You should not include the backslashes):

  globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf \ '&(jobtype=single)(count=4)(stderr=fa_pa.err)(stdout=fast34-HTC.out) \ (directory=/home/xxx/fasta)(executable=/usr/ngs/FASTA_34_26_5) \ (arguments=fasta34_t -H humanDNA2.input \"$DB_PATH\"/EBI/output/fasta/HTC 5)'

  • This runs the default version. To explicitly run v34.26.5 use FASTA_34_26_5 instead of FASTA.

   

Further Information

• FASTA Web site at Univ of Virginia
• Training Excersises