[Staden] gap4 running problem load_alignment_matrix gap.tcl line 674]

tmargus at ebc.ee tmargus at ebc.ee
Fri Aug 5 03:29:33 EST 2005

Hi again,

Could it be the question of installed LINUX distribution/version?
Different distributions default installation can be different, but what it
could be in my case I dont know.
I am using  Mandriva LINUX 2005 on dell's laptop D610 with mobile 1,6GHz 
32bit  processor.

Any helpe suggestions?


I have the same problem with Staden 1.5.3 on Ubuntu 4.10. but previous
version (Staden 1.4.1) works OK. Jan

Jan Matiasovic
Veterinary Research Institute
Czech Republic

>I am beginner in using staden and first I fall in to problems with
installing/running it.
>All staden folders are copied in /usr/local/bin/staden
>and following lines are added to .bashrc
>STADENROOT=/usr/local/bin/staden; export STADENROOT
>source $STADENROOT/staden.profile
>But when I running gap4 I got followin error
>[tmargus at localhost ~]$ gap4
>invalid command name "load_alignment_matrix"
>    while executing
>"load_alignment_matrix       [keylget gap_defs ALIGNMENT.MATRIX_FILE]"
>    (file "/usr/local/bin/staden/lib/gap/gap.tcl" line 674)
>Any help and suggestions are welcome
> Tõnu Margus
>Tartu university
>Riia 23
>Tartu 51010
>Staden mailing list
>Staden at net.bio.net

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