jalview v1.12.2b2 @bioconda

Jalview Discussion
1

Hi Jim,

I finished the Jalview recipe and wrapper for version 1.12.2b2.

   https://github.com/bioconda/bioconda-recipes/pull/6605

The package gets currently build and jalview should be available via bioconda within an hour. I will test the commandline-interface somewhen this week within our postprocessing pipeline.

What is left for you? Updating with upcoming releases.. :slight_smile:

To this end:
1) login to github
2) edit the jalview recipe at
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/jalview/meta.yaml
  2.1) update version
  2.2) update source:fn
  2.3) update source:url
  2.4) update source:sha256 (you can use https://md5file.com/calculator)
3) this change in (2) should trigger automatically a forking and pull request
4) wait whether the tests run fine
5) ping me @martin-mann and I or some colleague will merge the commit, which brings the new version online!

What else? You might want to change the description information in the meta.yaml using the same procedure from above.

Looking forward to see v1.13.0 at bioconda! :slight_smile:

Thanks,
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

2

Morning, Martin.

I finished the Jalview recipe and wrapper for version 1.12.2b2.

   Jalview v1.12.2b2 by martin-raden · Pull Request #6605 · bioconda/bioconda-recipes · GitHub

This is great news !

The package gets currently build and jalview should be available via
bioconda within an hour. I will test the commandline-interface somewhen
this week within our postprocessing pipeline.

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)

2. Memory - I've hacked a script that will max out the memory allocated
to Jalview.

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}

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 ?

I can submit a PR straight away for most of these, but should I do this
via bioconda's repo directly, or via your fork ?

Jim

···

On 06/11/2017 10:56, Martin Raden wrote:

3

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

  Jalview :: Anaconda.org

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

4

OK.

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](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 :wink:
j.

···

On 06/11/2017 12:50, Martin Raden wrote:

-- 
-------------------------------------------------------------------
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](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)