Cap3 assembly problem

2006-05-14
2013-04-18
  • I am trying to run pregap using a CAP3 assembly on my Mac. I've downloaded the cap3.osx folder, and I put cap3 and formcon on /usr/local/bin (which is in the PATH). However, when running the pregap modules I get the following message:

    cap3_assemble::init :cap3_s is not in user's path

    Any ideas on what is going on?

    I'd really appreciate any ideas/comments you might have. I've been unable to compile gcphrap and I am stuck!

    Thanks a lot in advance,

    /Jose Andres

     
    • funny, I am just doing the same thing, and came up with the same error. The program is expecting the file name cap3_s, so I simply renamed cap3 to cap3_s and it is recognised.
        I then get a problem in use as there should be an output file of file-names (.fofn file) which doesn't get produced, so it gets stuck. In the manual description of cap3 for use with pregap4, two program names are:  cap3 s and cap3_create_exp_constraints, but the files you get after unzipping the cap3 distribution are: cap3 and formcon. I cannot find any specific information about configuring these for OS X, but maybe if I play around with the cap3 options window it can be massaged to do the right things.
      MDS

       
    • James Bonfield
      James Bonfield
      2006-05-19

      There's two versions of Cap3; the standard one and one that was modified to create Experiment files (ie cap3_s). It has different arguments too.

      You need to obtain cap3_s in order for pregap4 to work.

      Yes I know it's a bit of a bad way of doing things - ideally we should have wrapped up the standard cap3 instead of extending the cap3 source, as with hindsight it means we've been unable to keep up to date with it at all.

      James

       
    • I can't see where to get cap3_s. When I go to the cap3 web site and fill out the form, all I get access to is cap3 and pcap. I note there is a new version of pcap called pcap.rep, that works more efficiently than previous versions (described in: http://seq.cs.iastate.edu/pub/papers/201.pdf\). Any chance of integrating that?
      MDS

       
    • OK, I've just had an email from the maintainer of CAP3. There is no current version of cap3 for gap4, and the advice is to use consed to view cap3 (or the current versions, pcap or pcap.rep) assemblies. To view cap/pcap/pcap.rep assemblies under consed you need to use the -nophd flag.
      So, it looks to me like the cap3 option should be removed from the current staden package.
      Mike Dyall-Smith