[Debian-med-packaging] Bug#815176: staden: Gap4 contig editor does not show sequences

[Andreas Tille]

On Mon, Feb 22, 2016 at 05:22:17PM +0100, Kerstin Hoef-Emden wrote:
> 
> Hi to all,
> 
> On Mon, 22 Feb 2016, Andreas Tille wrote:
> 
> >Hmmm, lets hunt down this as well.  Could you please write the output of
> >
> >   apt-get policy staden
> 
> You probably mean apt-cache policy staden?

Sorry, yes.
 
> khe at euler:~$ apt-cache policy staden
> staden:
>   Installiert:           2.0.0+b10-1.1
>   Installationskandidat: 2.0.0+b10-1.1
>   Versionstabelle:
>  *** 2.0.0+b10-1.1 0
>         500 http://ftp.de.debian.org/debian/ jessie/main amd64 Packages
>         100 /var/lib/dpkg/status
> 
> Actually I tried update and upgrade first, which did not include staden,
> then I deinstalled staden and reinstalled it.

That's the old buggy version. :-(

Did you tried

    apt-get update

first.
 
> >   cat `which pregap4`
> 
> Do you really want to see the whole script?

This just means you are using the previous version which has not
the mentioned bug fix yet.  You should use at least

     2.0.0+b10-2
              ^^
 
> >Perhaps you try
> >
> >   cp `which pregap4` ~/pregap4
> >
> >edit ~/pregap4 and add
> >
> >   set -x
> 
> Did not work.

Yes, that's clear since you are working on the old stuff.
 
> >as the second line in this script.  For me this looks pretty sensible.
> >
> >Alternatively you could try explicitly calling
> >
> >   /usr/lib/staden/bin/pregap4
> >
> >What happens if you do this?
> 
> Did not work (I am surprised - this is the path containing all modules).

Yes, this is where all modules reside and where they need to be found.

Thanks for helping to debug

    Andreas.


-- 
http://fam-tille.de