OK.
On 06/11/2017 12:50, Martin Raden wrote:
> you can just change the java version dependency to ">=7,<9"
I'd rather we didn't force unnecessary installs. jalview works fine with
1.9, providing the args are correct. By the way, how is JVM arbitration
managed in Conda ? I can't see any docs about that.
>
>> 2. Memory - I've hacked a script that will max out the memory allocated
>> to Jalview.
> ? you can add the patch to the recipe, no prob
people will need this - you may run into issues with it in your own
pipeline.
>
>> 3. Version numbers. Jalview's versioning is 'semi-semantic' - and
>> traditionally, distributions built via package management systems should
>> include the package version (so we can distinguish packager specific
>> issues).
>>
>> It's trivial to embed the version string, but I'd like to know what the
>> 'recommended' conda approach is here. e.g. can we just have
>> 2.10.2b2-conda${BUILDNUM}
>
> not sure if I get your question.. the build number is automatically
> added to the bioconda package. see "Files" in
>
> https://anaconda.org/bioconda/jalview
>
> So I am not sure if you have to do something special here..
the build number is also written into artefacts - and reported in log
files and the Jalview GUI, so it needs to be passed in to the build.
>
>> 4. Interactive use. You've packaged jalview for headless operation - is
>> there going to be any interest in having Jalview launch as an
>> interactive tool ?
>
> mhh.. I guess that you can use Jalview's GUI if you install the bioconda
> package on a system with X. I have removed the awt-tweak with my last
> commits. So I guess that's fine.
thanks !
> Thanks for the invitation to your bioconda fork. I have created a
> "jalview" branch and put the jdk version <9 tweak from above (1) and
> created a PR for communication.
>
> Feel free to add further and reopen the pull request for testing and
> merging.
will do. just as github lets my IP log in again ;)
j.
--
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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk
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