pregap4

2012-06-26
2014-08-01
  • Kim McKendrick
    Kim McKendrick
    2012-06-26

    I'm a complete beginner with Staden. I want to use pregap4 and have recently installed the windows version staden-windows-2.0.0b9.msi. I can run gap5 and trev but although I can see pregap4 files none of them are program files. Am I missing something or is pregap4 not included? Thanks very much for your help.

     
    • charles
      charles
      2014-08-01

      Hi please this is the first time i am using staden package, i think its good, but i got the following error below from the pregap4 tool.i am using windows. what am i not doing right.
      Just that you know, i have sanger sequence of SNPs that i am trying to validate. so i have wildtype and mutant.

      • Report from 'Gap4 shotgun assembly' -
        ERR: Failed to open database WILDTYPE.0.
        ERR: ""
        ERR: Aborting.
       
  • Hello,

    I did a clean install on a Windows XP machine and pregap4 worked fine, both from the Start menu and the bin directory where the Staden Package executables are stored.

    I'm not sure what to suggest.  Does pregap4.exe exist on your machine?

    Andrew

     
  • Kim McKendrick
    Kim McKendrick
    2012-06-27

    Hi Andrew, thanks very much for your help. I installed in Windows 7 so I retried in virtual XP but got the same result. The only executables I had were gap4.exe, gap5.exe and trev.exe. When I tried to run gap4.exe I got a message saying a tcl file was missing, which made me wonder so I renamed gap4.exe to pregap4.exe and double clicked and pregap4 opened - ?? I retried in Windows 7 and got the same thing - if I renamed the gap4 file to pregap4 then I get pregap4 version 1.6-r2852M.

    Kim

     
  • Hi Kim,

    You are right.  I downloaded the installer that is on SourceForge and used that instead of my development version.  The version on SF does not work properly.  I'll have to find out what went wrong and fix the installer.

    The .exe files that run the tcl/tk programs on Windows are a kind of trick.  They are all the same program but run different scripts depending on the name of the file.  So gap5.exe runs gap5, pregap4.exe runs pregap4 etc.  The odd one out is gap4 which needs a the program to be called gap.exe rather than gap4.exe (for historical reasons).

    So to fix your current problems, rename gap4.exe to gap.exe then make a copy and call it pregap4.exe.

    Thank you for bringing this to my attention.

    Andrew  

     
  • charles
    charles
    2014-08-01

    i please this is the first time i am using staden package, i think its good, but i got the following error below from the pregap4 tool.i am using windows. what am i not doing right.
    Just that you know, i have sanger sequence of SNPs that i am trying to validate. so i have wildtype and mutant.
    - Report from 'Gap4 shotgun assembly' -
    ERR: Failed to open database WILDTYPE.0.
    ERR: ""
    ERR: Aborting.