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

[Andreas Tille]

On Mon, Feb 22, 2016 at 03:25:11PM +0100, Kerstin Hoef-Emden wrote:
> 
> Hi to all,
> 
> at what time intervals syncing takes place?

12h if you are lucky - 24h is safe.

> I just tried pregap for the fix
> of the missing links and it did not yet work.

Hmmm, lets hunt down this as well.  Could you please write the output of

    apt-get policy staden
    cat `which pregap4`

Perhaps you try

    cp `which pregap4` ~/pregap4
    
edit ~/pregap4 and add

    set -x

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?

> I tested uncommenting the line in the tcl-script of the contig editor with a
> version downloaded from sourceforge and installed with stow and the fix
> worked (I use xfce4).

Sounds promising

    Andreas.

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