Gap5 and Caftools

  • Nobody/Anonymous

    I tried the new gap5 I installed it and the main window appears, trying to convert my gap4 project by gap2caf-->caf2baf seems it needs, I had it on my computer, linked by "use lib '/path/to/' " in the script, an old one I have.... but  now the script says that

    Can't locate object method "get_assembled_from" via package "Caftools" (line 23 (more or less))

    Somebody know where to found the correct I suppose mine is too old and this object method is not implemented.

    Thank you in advance,

    I am happy to try gap5.

    • Sven Klages

      Sven Klages - 2009-04-08

      Just download it from sanger,

      It's part of the miniphrap2gap package.


    • James Bonfield

      James Bonfield - 2009-04-08

      I'd forgotten I have had caf2baf lurking in that installation still.

      You won't really gain much going from gap4 to gap5 and you'll lose a lot. The main purpose of gap5 is to deal with the things that gap4 cannot - specifically VAST quantities of data. Over time the more useful gap4 abilities will migrate of course.

      That said getting gap4 DBs in gap5 is a good way to test the features (or lack of) :-)


      PS. Latest changes since the test release have been to fix the "pack sequences" view of the editor so the cursor manipulation works. I've also come up with a way for the names panel to still be useful in this mode too, rather than simply displaying misleading data.

    • Giuseppe D'Auria

      Ok, thank you it worked I suppose fine,

      I work with 454 assemblies and from what I read, gap5 have important improvements about new hightroughput technologies.

      more problems...

      running tg_index following the README, or simply executing tg_index, I always have back the same error:

      tg_index: error while loading shared libraries: cannot open shared object file: No such file or directory

      the file is in the same directory of tg_index and reached by the path.

      I do not know what is wrong. I forgot to say that I am under Ubuntu 64bits

      thank you in advance


    • James Bonfield

      James Bonfield - 2009-04-09

      The should be in the lib/linux-x86-binaries subdirectory along with a whole load of other required libraries. You can add this manually to your LD_LIBRARY_PATH environment variable and it should find it.

      In theory the tg_index and tg_view programs are wrappers to set this up automatically and then run tg_index.bin and tg_view.bin in much the same way that the gap5 program is a wrapper to do this and run stash. It seems my last install broke that though and I didn't notice as my LD_LIBRARY_PATH includes those directories anyway.

      So either manually set LD_LIBRARY_PATH or replace tg_index with this script.



      # Finds the directory holding this program
      find_dir() {

          # Protect against ls, sed and echo being exported shell functions.
          # Eg ls() { ls -F ${@+"$@"} }; export ls
          unset ls
          unset sed
          unset echo


          # The looping is to protect against symbolic links. We find the location
          # of arg0, but if arg0 is a link to elsewhere then we go around again
          # finding its location (noting that symlinks may be ether relative
          # or full pathnames).
          while [ -n "$must_loop" ]

              # Find directory that $arg0 resides in
              case $arg0 in
                      # Full pathname, not much to do
                      dir=`echo $arg0 | sed 's:/[^/]*$::'`
                      # Relative pathname, add current directory.
                      dir=`echo $cur_dir/$arg0 | sed 's:/[^/]*$::'`

              if [ -h $arg0 ]
                  # NOTE: This statement will not work when $arg0 is a filename
                  # containing "-> ".
                  lnto=`ls -l -- $arg0 | sed 's/.*-> //'`
                  lndir=`echo $lnto | sed 's:/[^/]*$::'`
                  case $lndir in
                          # Absolute symlink
                          # Relative symlink
                          dirto=`echo $arg0 | sed "s:/[^/]*\$:/$lndir:"`

                  cd "$dirto"
                  arg0=`echo $lnto | sed 's:.*/::'`

          # To tidy up cases with ../ and ./ we cd to the directory, getcwd, and then
          # cd back again
          cd "$dir"
          cd "$orig_dir"

          echo $dir

      STADENROOT=`find_dir $0`/..
      export STADENROOT
      STADEN_PREPEND=1 . $STADENROOT/staden.profile

      # Define TCL/TK config - not defined in staden.profile as it may break
      # some other applications the user wishes to use.

      # Run it!
      exec tg_index.bin ${@+"$@"}

    • James Bonfield

      James Bonfield - 2009-04-09

      Ugh, wish there were attachments on these forums. Well if it doesn't work let me know and I'll upload it to the patches area or similar.

    • Giuseppe D'Auria

      Ok, I changed tg_index whit the script you pasted here and it works perfectly.
      I was able to load my db (big 454 db whit Paired Ends)
      Now I start testing the program.....

      do you think this is the good forum to chat about the program?



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