Some help required.
Qingjuan Gu
qingjuan at wistar.upenn.edu
Tue Jul 30 14:27:36 UTC 2002
The possible reason for this: your 'real database' have permission problem, double-check your 'tembl' database mod.
---------- Original Message ----------------------------------
From: Alex Brown <abrown at nimr.mrc.ac.uk>
Date: Tue, 30 Jul 2002 14:36:27 +0100
>Hi.
>
>Firstly, let me apologize for what may seem a trivial problem, but I
>have nowhere else to turn. I have 'used' UNIX previously, but only as a
>user (and not very often at that), and not as an administrator, and the
>problem is getting EMBOSS to function properly.
>
>I have installed EMBOSS on a Macintosh PowerBook G4, under Darwin. I am
>also running XDarwin (XFree86 4.2.0). After installation and running
>'make install', 'wossname -auto | less' gives a long list of programs,
>as stated in the EMBOSS Administrators Guide, section 2.3.5.
>
>All the program files are located in the /usr/local/bin directory - I
>notice that there is no EMBOSS entries in /usr/share/man. Is this
>correct ?
>
>In order to get the 'showdb' command to list the available databases, I
>uncommented the first line of the emboss.default.template file (SET
>emboss_tempdata path_to_directory_$EMBOSS/test) and copied this to
>emboss.default. The command 'showdb' results in the following output:
>
># Name Type ID Qry All Comment
># ==== ==== == === === =======
>tpir P OK OK OK PIR using NBRF access for 4 files
>tsw P OK OK OK Swissprot native format with EMBL CD-ROM
>index
>tswnew P OK OK OK Swissnew as 3 files in native format with
>EMBL CD-ROM index
>twp P OK OK OK EMBL new in native format with EMBL
>CD-ROM index
>tembl N OK OK OK EMBL in native format with EMBL CD-ROM
>index
>tgb N OK - - Genbank IDs
>tgenbank N OK OK OK GenBank in native format with EMBL CD-ROM
>index
>
>indicating the databases in the /local/share/EMBOSS/test directory.
>
>So far so good.
>
>However, attempting to work through the tutorial on the EMBOSS web-site,
>I find that I am unable to access the databases: for example
>
>[xxxxxx:~] me% seqret
>Reads and writes (returns) sequences
>Input sequence(s): tembl:hs*
>Warning: Cannot open division file '<null>'
>Warning: seqCdQry failed
>Error: Unable to read sequence 'tembl:hs*'
>Input sequence(s):
>
>I was assuming that the databases that came with the installation would
>work, and would allow me to work round to installing my own databases.
>The above would indicate that there is still something I have yet to do.
>Could someone please offer me some guidance on this.
>
>Many thanks.
>
>Alex Brown.
>
>
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