Some help required.
abrown at nimr.mrc.ac.uk
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
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
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*'
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.
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