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Re: [Bio-linux-devel] phoenix clinical trial management system integration

[Removing bio-linux-devel@bioinformatics.org from CC since I understood Tony
 that it is not relevant for this list.]

Hi Rene,

On Tue, May 22, 2018 at 09:13:45AM +0200, Rene Krenn wrote:
> ok regarding packaging, jfyi this is the script to get (and build) it on a minimal debian 9.4 (or ubuntu 16.04):
> https://github.com/phoenixctms/install-debian/blob/master/install.sh

Its good to have this kind of script to have a plan what to do.
However, I see lots of wget calls there.  We need to make sure that
every needed component is available as Debian package - in other words:
We need to replace wget by apt-get.
> To get rid of outdated dependencies, we already moved on to OpenJDK8 successfully last week.
> The next task will be to ensure it works with more recent versions of tomcat.

Please note new packages are targeting at Debian unstable.  It has
currently tomcat 8.5.30 and OpenJDK 9.0.4.  I'm not a Java expert at all
and thus don't now what a OpenJDK8 to OpenJDK9 move might mean in
practice but some of the Debian Med Java packages needed adaptations to
> The perl-based ETL framework (https://github.com/phoenixctms/bulk-processor ) should most likely become a separate
> package.

This seems to be a pretty nice target to learn packaging.

> So i suggest there should be one package for the main tomcat webapp, and one for the bulk-processor.

This sound sensible.

> Another optional one would be the public subject signup portal, which is a perl dancer webapp.

I admit I have never heard about perl dancer but
   libdancer2-perl - lightweight yet powerful web application framework
is packaged so you can base upon this.

Kind regards

> -----Ursprüngliche Nachricht-----
> Von: Andreas Tille [mailto:andreas@an3as.eu] 
> Gesendet: Dienstag, 22. Mai 2018 08:02
> An: Tony Travis <tony.travis@abdn.ac.uk>
> Cc: bio-linux-devel@bioinformatics.org; Debian Med Project List <debian-med@lists.debian.org>; rkrenn@phoenixctms.org
> Betreff: Re: [Bio-linux-devel] phoenix clinical trial management system integration
> Hi,
> @Tony: Thanks a lot for forwarding this. :-)
> On Sat, May 19, 2018 at 02:56:18PM +0100, Tony Travis wrote:
> > On 18/05/18 23:19, Rene Krenn wrote:
> > > hello,
> > >
> > >
> > >
> > > would like to probe if there is an interest to include 
> > > https://github.com/phoenixctms ?
> > >
> > > it’s the most powerful EDC system we know.
> > >
> > >
> > >
> > > pls let me know if it makes sense and someone can/wants to help with 
> > > packaging.
> For sure we would love to help you in packaging.  We have quite some record in teaching upstream how to package.  We have formalised this process in so called "Mentoring of the Month" (MoM)[1].  You are more than welcome to add yourself to the list of students (or simply confirm here on this list[2] if you are scared by just another random Wiki login in the web.  However, you should subscribe in any case this list since the mentoring is done in public.)
> > Hi, Rene.
> > 
> > Bio-Linux is a platform for bioinformatics, rather than collecting and 
> > analysing clinical trials data.
> It looks like a good target for the task "Research"[3] which has no existing package yet which is a real shame - but may be you consider other of our tasks[4] fitting better / in addition.
> > However, many packages from Debian-Med are included in Bio-Linux and 
> > the two projects work together to avoid duplication of effort 
> > packaging the same bioinformatics software.
> > 
> > The Debian-Med project is much broader than Bio-Linux and specifically 
> > includes biomedical applications like your clinical trials management 
> > software. I've CC'ed your message to the Debian-Med mailing list so we 
> > can discuss the possibility of packaging your software there.
> > 
> > Please post a message to the Debian-Med list explaining clearly what 
> > the licence is for your software and what, exactly, you want to package.
> Nothing to add to Tony's kid explanation.
> Kind regards
>         Andreas.
> [1] https://wiki.debian.org/DebianMed/MoM
> [2] https://lists.debian.org/debian-med
> [3] https://blends.debian.org/med/tasks/research
> [4] https://blends.debian.org/med/tasks
> --
> http://fam-tille.de


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