[Staden] using emboss programs from spin

Miguel Ortiz Lombardia via staden%40net.bio.net (by mortiz from cnio.es)
Thu Oct 19 06:36:35 EST 2006

Dear all,

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

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 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: molatwork from yahoo.es
www: http://www.ysbl.york.ac.uk/~mol/
Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie.                          (Raoul Vaneigem)

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