[EMBOSS] [Jemboss] needle Jemboss on MacIntosh

[ajb at ebi.ac.uk]

Is this a case of running a Jemboss client on the Mac but the
Jemboss server on a UNIX machine?

If that is the case then the problem is likely to be that your
input files have lines terminated with '\r' whereas the server will
be expecting them to terminate with '\n'.

EMBOSS does cater for '\r'-terminated files but only if EMBOSS
itself is compiled under MacOSX PPC.
The first thing to try would be for you to convert the files i.e.
under UNIX you could use:

  tr '\r' '\n' < macfile > unixfile

to do it. Then try giving the UNIX-formatted file to the server.

We could arrange for EMBOSS to always detect whether UNIX (LF),
Mac (CR) or M$ (CRLF) user files are given but it'd be a performance hit.
One way would be to provide it as an EMBOSS configuration option.
We'll discuss it anyway.


HTH

Alan



>
> Running Jemboss on a Mac.
> I have a folder of GCG sequences, one of which I have included.
> When I open these files in textedit, they are complete.
> However when double clicked in the file manager, they look like fasta
> files
> with no sequence information. Likewise when input to a program like
> needle.
> It doesn't seem to matter what is done with Input Sequence Options.
>
> What's Up, Doc?
>
>
>
> Nick Staffa
> Telephone: 919-316-4569  (NIEHS: 6-4569)
> Scientific Computing Support Group
> NIEHS Information Technology Support Services Contract
> (Science Task Monitor: Roy W. Reter (reter at niehs.nih.gov)
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina
>
>
>
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