Some help required.

Qingjuan Gu qingjuan at
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>
Date:  Tue, 30 Jul 2002 14:36:27 +0100

>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 
>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 
>tgb           N    OK  -   -   Genbank IDs
>tgenbank      N    OK  OK  OK  GenBank in native format with EMBL CD-ROM 
>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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