Some help required.

Alex Brown abrown at
Tue Jul 30 13:36:27 UTC 2002


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 
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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