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
