JalView @ bioconda ?!

Jalview Developers
1

Hi Martin - I’m cc-ing our development mailing list for posterity.

we are planning to use JalView in our upcoming new CopraRNA postprocessing pipeline to visualize alignments with additional annotations, for which we found JalView very well placed. Thanks for the tool!

Thanks very much :slight_smile:

Since we are distributing our tool via the bioconda platform, we would like to know whether you are aware of this platform and if you are interested to provide JalView also this way?

We have indeed been considering bioconda as a distribution route.

https://bioconda.github.io/

Bioconda is currently the most extensive bioinformatics software distribution platform and enables easy to use installation of about 3000 tools. If you would integrate JalView here, its visibility, availability and usage is much increased, since it could be installed via a common interface and also easily integrated/provided as dependency for other tools (like CopraRNA).

This is another excellent reason for us to connect with bioconda downstream.

We could help with the setup of an initial bioconda ‘recipe’, while the update to new releases would have to be done by you via github.

That would be a great help indeed !

One detail is that we do not coordinate jalview development via github. Instead, we manage our development and repositories via issues.jalview.org/git.jalview.org (though we plan to mirror via https://github.com/jalview in the very near future).

I’m happy to spawn a jalview-bioconda distro repository on the jalview github org, but for admin simplicity we will need to ensure that bug reports are passed into our own issue tracker. Does bioconda require packaging work to be coordinated solely via github ?

Jim.

The University of Dundee is a registered Scottish Charity, No: SC015096

···

On 02/11/2017 15:47, Martin Raden wrote:

-- 
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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](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
2

Please see Martin’s reply below.

Hi Jim,

thanks for the prompt reply and good to hear that you are interested in bioconda! That would be really cool!

About the issues you mentioned: no problem! Here a few details about the distribution workflow with bioconda, so you will see that it well fits with your current setup.

  1. create your distribution and host it somewhere online
  2. create a “jalview” subfolder in a fork/branch of
    https://github.com/bioconda/bioconda-recipes
  3. create a “meta.yaml” description file for your tool that sums up dependencies, version information, where to download the package from (would be point (1)), what dependencies there are, a small test call, etc…, eg. see

https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/meta.yaml
4) create a “build.sh” file that unpacks and installs your tool package, eg. see

https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/meta.yaml
there are a few hints how this should be done for java tools.
https://bioconda.github.io/guidelines.html#java
5) create a pull request, which triggers sanity checks and testing of your recipe. if all goes well it gets merged and jalview is available via bioconda within a few hours.

All tool development, issue tracking, etc. is totally independent from bioconda and github, so no worries here. Links are provided in the meta.yaml file.

Since a tool is only as good as it is up-to-date, I was pinging you whether you are interested to extend you jalview distribution to bioconda and keep it updated. the latter would mean to update (3) and (5) with every jalview release, which is not much of work but still something to be done.

So I think we could get this running quite easily. The only question is what your installer is doing in the end (didnt had a closer look so far), since bioconda has a clear procedure where java JARs are to be stored and how to wrap the tool to avoid “java -jar XYZ” calls.
https://bioconda.github.io/guidelines.html#java
Might need some workaround here, but as I said, I didnt had a closer look yet.

If you are interested, let me know and I will start with (2-4) and send you the github pull request. Just send me your github user name and I will give you write access to the according branch.

Looking forward to get this running!

Best,
Martin

Hi Martin - I’m cc-ing our development mailing list for posterity.

we are planning to use JalView in our upcoming new CopraRNA postprocessing pipeline to visualize alignments with additional annotations, for which we found JalView very well placed. Thanks for the tool!
Thanks very much :slight_smile:
Since we are distributing our tool via the bioconda platform, we would like to know whether you are aware of this platform and if you are interested to provide JalView also this way?
We have indeed been considering bioconda as a distribution route.
https://bioconda.github.io/

Bioconda is currently the most extensive bioinformatics software distribution platform and enables easy to use installation of about 3000 tools. If you would integrate JalView here, its visibility, availability and usage is much increased, since it could be installed via a common interface and also easily integrated/provided as dependency for other tools (like CopraRNA).
This is another excellent reason for us to connect with bioconda downstream.
We could help with the setup of an initial bioconda ‘recipe’, while the update to new releases would have to be done by you via github.
That would be a great help indeed !

One detail is that we do not coordinate jalview development via github. Instead, we manage our development and repositories via issues.jalview.org/git.jalview.org (though we plan to mirror via https://github.com/jalview in the very near future).

I’m happy to spawn a jalview-bioconda distro repository on the jalview github org, but for admin simplicity we will need to ensure that bug reports are passed into our own issue tracker. Does bioconda require packaging work to be coordinated solely via github ?

Jim.

The University of Dundee is a registered Scottish Charity, No: SC015096

···

On 03/11/2017 09:54, 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)