Hi Jim,
> I also tested your conda patch over the weekend, and noticed a few issues:
>
> 1. Java 9 compatibility (the java command line is different if java 9 is
> installed)
you can just change the java version dependency to ">=7,<9"
> 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
> 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..
> 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 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.
Best,
Martin
--
Dr. Martin Raden, nee Mann, Postdoc
Bioinformatics - Prof. Dr. R. Backofen
Department of Computer Science
Albert-Ludwigs-University Freiburg
Add: Georges-Koehler-Allee 106, room 02012, 79110 Freiburg, Germany
Tel: ++49-761-203-8254 (Monday-Wednesday)
Fax: ++49-761-203-7462
http://www.bioinf.uni-freiburg.de/~mmann/
Forest Growth and Dendroecology
Institute of Forest Sciences
Albert-Ludwigs-University Freiburg
Add: Tennenbacher Str. 4, room 02062, 79106 Freiburg, Germany
Tel: ++49-761-203-3733 (Thursday+Friday)
Fax: ++49-761-203-3740
http://www.iww.uni-freiburg.de
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