Re: IGV

[Andreas Tille <andreas@an3as.eu>]

Hi Tony

On Tue, Oct 16, 2018 at 12:27:26AM +0100, Tony Travis wrote:
> Hi,
> 
> The "igv" package imported from Debian-Med does not work correctly under
> Ubuntu-MATE 18.04 LTS:
> 
> > lsb_release -d
> > Description:	Ubuntu 18.04.1 LTS
> > apt-cache policy igv
> > igv:
> >   Installed: 2.4.6+dfsg-1
> >   Candidate: 2.4.6+dfsg-1
> >   Version table:
> >  *** 2.4.6+dfsg-1 500
> >         500 http://gb.archive.ubuntu.com/ubuntu bionic/multiverse amd64 Packages
> >         500 http://gb.archive.ubuntu.com/ubuntu bionic/multiverse i386 Packages
> >         100 /var/lib/dpkg/status
> 
> I've posted a bug-report, and a patch to add
> "/usr/share/java/commons-io.jar" and "/usr/share/java/gson.jar" to the
> class path used by "igv":
> 
> > https://bugs.launchpad.net/ubuntu/+source/igv/+bug/1797819
> 
> Please note: I don't want the default to be Java 8 for Bio-Linux 9, so I
> forced "igv" to execute Java 8 directly using an absolute path. I'm sure
> there is a better way of doing that and I'd welcome your suggestions.

Currently Olivier and I are working on the new version of IGV.  I took
over the part of your patch with the missing classes[1] (thanks for the
hint).  I hope there will be a solution not to force a certain Java
version but the build seems to be tricky at the moment (see comments
from Olivier in d/changelog).

Kind regards

      Andreas.

PS: In general it is the best idea to fire up reportbug and report this
    kind of issues in the Debian BTS.
    Disclaimer: There are Debian maintainers who do not like this but for
    the Debian Med team that's perfectly fine.


[1] https://salsa.debian.org/med-team/igv/commit/39037318fb7938efdddf8632f5b91023c0e2046f

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