Re: [Bio-linux-dev] Bringing the Artemis package officially into Debian
Hello,
On الأربعاء 23 أيلول 2015 03:03, Steffen Möller wrote:
>
> On 23.09.2015 09:26, Andreas Tille wrote:
>> thanks again for your push on artemis packaging.
> Indeed. A big "wow!" also from my side.
>> On Tue, Sep 22, 2015 at 08:51:59PM -0700, Afif Elghraoui wrote:
>>> Following the earlier email exchange, I had started some draft packaging
>>> for Artemis [1]. At a cursory look, it seems that all the Java
>>> dependencies are now available from Debian packages.
> The onset of Artemis development kind of matched my time on
> the genome campus. I feel somewhat emotionally touched by your
> effort. Have many thanks, especially so since my personal attempts
> to work on Debian-proper packaging of Taverna (developed at about
> the same time) have turned out to be too difficult for me, maybe
> you at least benefit from the one or other contributed Java package :)
>
You just reminded me of the community-driven computational biology paper
that you all published [1]. I thought the principle was a great idea and
have some interest in following that up.
> More seriously, to have our distros preparing for the annotation
> of whole genomes is of exceptional importance. And the difficulties
> with Java dependencies also nags others, for sure.
>>> That is, except for
>>> jemAlign.jar, which I can find no trace of anywhere on the internet
>>> other than Artemis's bundle and an email thread on Debian Med where
>>> Andreas is also looking for its source. The Artemis upstream repository
>>> at github shows that the jar file is about as old as git itself, so I'm
>>> curious if it is still even necessary (or even works with modern Java
>>> versions).
>> Sometimes you simply find out by droping a *.jar whether it is needed or
>> not (but upstream confirmation would be better for sure). :-)
> I propose to contact Kim Rutherford about it. My favorite suspect,
> having looked at the classes of the jar, is that it is some version of
> jemboss providing the "Jemboss Alignment Editor". We have several
> folks on the Debian Med list that seem to have been involved with
> it in some way and who certainly reply once their subject line triggers
> their attention :)
Thanks for the tips.
>>> In any case, my draft package doesn't build right now, apparently
>>> because the classpath is not being read by javac.
>> I added jemboss as Build-Depends which reduced the number of "class not
>> found" errors. I also added citation data.
>>
Thanks, Andreas. I'll see what I can do.
>>> Did I mention I'm no Java enthusiast?
>> Did I mention that I'm in the same group?
> Still suffering.
>
:/
Thanks and regards
Afif
1. http://www.biomedcentral.com/1471-2105/11/S12/S5
--
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name
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