[Staden] gap4 running problem load_alignment_matrix error

[alig]

Hi,

I am trying to install Staden Gap4 on a 64 bit machine with Ubuntu
installed.

It appears that trev & pregap will start. But when I type gap4& I get this
message -

invalid command name "load_alignment_matrix"
while executing
"load_alignment_matrix [keylget gap_defs ALIGNMENT.MATRIX_FILE]"
(file
"/usr/local/staden-linux-x86_64-1-7-1b/linux-x86_64-bin/../lib/gap/gap.tcl"
line 683)

I have followed a number of suggestions from this site & others & installed
some missing libraries, but still get this message.
Have done strace -o output.txt gap4 and not sure of any more errors in that
file.
I will try to attach the file
http://www.nabble.com/file/p21740409/output.txt output.txt

Can anyone help please
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[Paul Donohue]

I don't see anything in particular in your strace output after a quick look.

Try running 'export STADEN_DEBUG=1' before running staden, and see what that says.
You can ignore the 'libiwidgets.so' error, but any other errors need to be fixed.

Note that you can use the 'Search the contents of packages' form at http://packages.ubuntu.com/ to figure out the appropriate package to install for any missing libraries.

Hope that helps.
-Paul

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[alig]

Thank you, that fixed it & now I can run Gap4 so I'm very happy.

This was the error I got after running 'export STADEN_DEBUG=1'

load libcopy_reads.so => couldn't load file "libcopy_reads.so":
/usr/lib/libstdc++.so.5: version `CXXABI_1.2' not found (required by
/usr/local/staden-linux-x86_64-1-7-1b/linux-x86_64-bin/../lib/linux-x86_64-binaries/libmutlib.so)

I had linked it to a newer version. So I unlinked & reinstalled libstdc++5
& that seemed to fix my problem.

Thanks again alig

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