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

[Andreas Tille]

Hi Kerstin,

On Tue, Feb 23, 2016 at 05:10:06PM +0100, Kerstin Hoef-Emden wrote:
> On Tue, 23 Feb 2016, Andreas Tille wrote:
> >
> >Kerstin, you can either download the staden packages from unstable from
> >here:
> >
> >  https://packages.debian.org/source/unstable/staden
> >
> >and install manually on your Jessie system
> 
> I had a look at the requirements in the README.build file. Manual install is
> not straightforward. Itcl, itk and iwidgets are not available for jessie.
> Also configure complains about a missing io_lib.

We are talking about different things when talking about "manual install".
You can download the packages manually via wget

   http://ftp.de.debian.org/debian/pool/main/s/staden/staden_2.0.0+b10-3_amd64.deb
   http://ftp.de.debian.org/debian/pool/main/s/staden/staden-common_2.0.0+b10-3_all.deb

any *may* *be* you might also need

   http://ftp.de.debian.org/debian/pool/main/s/staden-io-lib/libstaden-read11_1.14.7-1_amd64.deb

(if the libstaden-read11 from stable is not sufficient) and than do

   sudo dpkg -i *.deb

with the downloaded debs.  There is no point in following READM.build and
compile staden from the sources.

> >or you add unstable to your
> >/etc/apt/sources.list.  ATTENTION: You need to adapt
> >/etc/apt/preferences to make sure you will not bump your whole system
> >to unstable!
> 
> The most "dangerous" and possibly destabilizing actions I did, were
> installations of backports. I usually don't dare to touch sid. Probably the
> install will also result in the missing itcl etc. being installed? Will it
> work, if I restrict it as such?

You need to drop a file /etc/apt/preferences with the content

Package: *
Pin: release a=stable
Pin-Priority: 501

Package: *
Pin: release a=unstable
Pin-Priority: 50


(or if your /etc/apt/sources.list contains "jessie" instead of
 stable use this one with the priority 501)

> Package: staden
> Pin: release n=sid
> Pin-Priority: 900

Yes, this would pick staden from sid (== unstable) but the general
preferences file as I wrote above makes sure that no *other* packages
will be taken from sid.  You can even without the specific staden
pinning do:

   apt-get -t unstable install staden staden-common

Please always check

   apt-cache policy staden

before.  Moreover if some random

   apt-get update

might install *lots* of packages - you have messed up the preferences.

Hope this helps

       Andreas.

-- 
http://fam-tille.de