using emboss programs from spin

[Miguel Ortiz Lombardia]

Dear all,

I have installed on a linux system (Ubuntu 6.06):

Staden-1.7.0
EMBOSS 3.0.0

First, I had to make the iwidgets symbolic link in staden-1.7.0/lib to
point to the right place:

ln -sf /usr/lib/iwidgets4.0.1 iwidgets

I wanted to use the spin interface to run emboss programs. So I run
create_emboss_files. Because the tcl script assumes a wrong localization
of the acd files (and then it hangs indefinitely) I had to change the
create_emboss_files.tcl file so the script would know where such files
are in fact. This is what I did:

1. Comment out the procedure "proc acd_dir"

2. Down in the file change set acd_dir [acd_dir] to:
set acd_dir /usr/local/share/EMBOSS/acd

After doing this, the acd files are found and some of them processed.
Others produce errors, I can post these errors if someone is interested.

To use staden with emboss, I issued:

export STADENROOT=/usr/local/staden-1.7.0
. $STADENROOT/staden.profile
export EMBOSS_DATA=/usr/local/share/EMBOSS/data

But then I get many "qualifier" errors. I think this is because the
spin_emboss package instead of the spin2_emboss one is being used. I
checked at least that for the EMBOSS program "matcher".

Could someone tell me how to enforce the use of spin2_emboss?

Thank you very much in advance,

Miguel
--
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: mola...@yahoo.es
www: http://www.ysbl.york.ac.uk/~mol/
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[Guy Bottu]

Miguel Ortiz Lombardia <mor...@cnio.es> wrote:

> But then I get many "qualifier" errors. I think this is because the
> spin_emboss package instead of the spin2_emboss one is being used. I
> checked at least that for the EMBOSS program "matcher".

> Could someone tell me how to enforce the use of spin2_emboss?

I think the nature of your problem is different. create_emboss_files
contains a line
exec stash $STADLIB/spin2_emboss/create_emboss_files......
that tells the program to make files for spin2 ; you can replace this by
spin. spin2 is a successor program of spin, which however did not get
beyond alpha test because the cut of the support for the Staden team.
There is more serious : spin worked relatively well with EMBOSS 2.8 but
starting with EMBOSS 2.9 the syntax of the ACD files was changed and
since then under spin EMBOSS programs do not greyout optional parameters
as needed or simply do not run at all. I managed to make it work at the
BEN site, but only with a lot of ugly hacking....
Peter Rice from the EMBOSS team had promised to do some work on Staden
to make it again EMBOSS compatible, but he has a lot of other things to
do and I am afraid he did not yet come to it. Maybe you can send a mail
to the EMBOSS mailing list emb...@emboss.open-bio.org

Regards,
Guy Bottu,
Belgian EMBnet Node

[Peter Rice]

Guy Bottu wrote:
> Peter Rice from the EMBOSS team had promised to do some work on Staden
> to make it again EMBOSS compatible, but he has a lot of other things to
> do and I am afraid he did not yet come to it. Maybe you can send a mail
> to the EMBOSS mailing list emb...@emboss.open-bio.org

Yes please ... we would very much like to know how many Staden users are
interested in the EMBOSS interface.

I plan to update it for EMBOSS 4.0.0 (released last July).

regards,

Peter