Re: IGV update - any takers?

[Olivier Sallou <olivier.sallou@irisa.fr>]

On 11/13/19 1:42 PM, Steffen Möller wrote:
> Hello,
>
> One of the packages that Debian should really shine with is IGV - it is
> used throughout the world to inspect RNAseq data. And the ones running
> IGV are not the ones who ran the analysis, so there should be tons of
> folks out there using it who are not already installing conda in
> routine. Admittedly, those will mostly be Windows/MacOS users, but hey,
> also some Debianers. Popcon only lists one installation. Something must
> be wrong. We are a bit behind with its version (2.4) with 2.7 being the
> latest, but also conda only has 2.5 to offer, so that is likely not the
> reason.

I had a quick look at latest version. It seems to be have been rewritten
a lot, a lots of dependency differences.

Several java (maven) libs are not available in debian or older (may work
or not):


       Not available [group: 'org.campagnelab.goby', name: 'goby-io',
version: '3.3.1']
       Not available [group: 'org.campagnelab.icb', name: 'icb-utils',
version: '2.0.2']

      older version in debian (libjsap-java) [group:
'org.campagnelab.ext', name: 'jsap', version: '3.0.0']

      older version in debian (libnb-absolutelayout-java) [group:
'org.netbeans.external', name: 'AbsoluteLayout', version: 'RELEASE110']

        Not available [group: 'software.amazon.awssdk', name:
'http-client-spi', version: '2.8.5'],
        Not available [group: 'software.amazon.awssdk', name:
'cognitoidentity', version: '2.8.5'],
        Not available [group: 'software.amazon.awssdk', name: 'sts',
version: '2.8.5'],
        Not available [group: 'software.amazon.awssdk', name: 's3',
version: '2.8.5']


Olivier


>
> I just found it to be in conflict with R libraries I had on my system
> because of dependencies on different versions of libhdf-dev - somewhat
> unexpected. The changelog found Sascha, Andreas and Olivier as past
> active maintainers. Do you have further insights for me? And - is IGV a
> reasonable package to be backported?
>
> Regards,
> Steffen
>
-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438