Gap5 and Caftools

[Nobody/Anonymous]

Hi
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 Caftools.pm, I had it on my computer, linked by "use lib '/path/to/Caftools.pm' " 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 Caftools.pm 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]

Just download it from sanger,

http://www.sanger.ac.uk/Software/formats/CAF/

It's part of the miniphrap2gap package.

cheers,
Sven

[James Bonfield]

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) :-)

James

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: libtgap.so: cannot open shared object file: No such file or directory

the file  libtgap.so 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

Giuseppe

[James Bonfield]

The libtgap.so 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.

James

#!/bin/sh

# Finds the directory holding this program
find_dir() {
    arg0=$1

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

    orig_dir=`pwd`
    must_loop=yes

    # 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" ]
    do
        cur_dir=`pwd`

        # 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:/[^/]*$::'`
                ;;
        esac

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

            cd "$dirto"
            arg0=`echo $lnto | sed 's:.*/::'`
            must_loop=yes
        else
            must_loop=
        fi
    done

    # To tidy up cases with ../ and ./ we cd to the directory, getcwd, and then
    # cd back again
    cd "$dir"
    dir=`pwd`
    cd "$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.
TCL_LIBRARY=$STADLIB/tcl
TK_LIBRARY=$STADLIB/tk
export TCL_LIBRARY TK_LIBRARY

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

[James Bonfield]

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?

Giuseppe