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: molatwork from yahoo.es
www: http://www.ysbl.york.ac.uk/~mol/
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