Hi Aaron, On Wed, Apr 29, 2015 at 11:41:53PM +1000, Aaron Darling wrote: > Hi Andreas, it's really exciting to hear that you're taking another stab > at this. More below.
Great to hear this. While this is the usual response of upstream developers it is not always the case. Thanks also for responding that quickly. > > The oldest package in Debian is libgenome version 1.3.1 which resides > > inside Debian since 25 Jun 2008 when it could be downloaded from the > > formerly used website[2]. This site does not exist any more but the > > source code is available from sourceforge[3]. I have no idea whether > > there are some important changes in trunk. In any case it would be > > helpful to do some release (of any of your relevant libraries and tools) > > to be downloadable from the Files section of the SourceForge page. > > ok, there have been a few small changes. some minor bugfixes but nothing > major but i'd be happy to put a new release up -- it's overdue. Cool. It would be really appreciated it you ping this mailing list about new releases and we try to respond with a package upload in a short time frame. > > Recently I have added libmuscle (version 3.7) and libmems (version 1.6) > > to the Debian pool. I have created a tarball from the latest trunk. > > Also here a proper versioned release would be really helpful. The > > rationale is that there is a Debian tool that checks websites for > > regular expressions whether new versions might have shown up. This tool > > can be easily pointed to the Files section of SourceForge but it does > > not work properly on SVN commit IDs. > > ok, can do this too. Thanks. That's very helpful. > > After some patches[5] I was able to fully delete the build_support/ dir > > in the source dir. Debian contains the needed tools to build Mauve > > successfully - so I was able to get rid of it. > > ok, i'll try to look at the changes in the coming days and confirm > nothing obvious has broken. :-) > > Now to the JAR files in the ext/ directory. I noticed that you are > > providing BioJava 1.9.2-SNAPSHOT in three different JAR files: > > bytecode-1.9.2-SNAPSHOT.jar, core-1.9.2-SNAPSHOT.jar and > > gui-1.9.2-SNAPSHOT.jar. Debian contains BioJava in only one JAR file > > and this was used to build the package. The possibly weak part is that > > Debian has stalled on version 1.7.1 of the BioJava 1.x series. I know > > that BioJava 3.x is not fully compatible with the 1.x series but I > > wonder > > > > a) Is 1.9.2 really required or is 1.7.1 fine as well for Mauve? > > b) Do you intend to convert Mauve to BioJaba 3.x? > > > > Depending from your answer the BioJava dependency might need some work > > from our side. > > well, the issue is even more complicated because I've patched the > biojava 1.9.2 code to fix an incompatibility with parsing GenBank format > files produced by the prokka software. So without that patch this > functionality will break. I am not sure if the patch can be applied to > 1.7.1. There is also a potential GUI issue regarding the responsiveness > of tooltips over annotation tracks in 1.7.1. I admit that I have basically zero knowledge of Java and need to rely on the expertise of other members of the Debian community. Considering Oliviers mail about BioJava 4 at least my gut feeling says it might be sensible to use the latest supported upstream version and thus porting Mauve to BioJava 4 would something I'd consider. But take this idea with a grain of salt from an admittedly poorly educated person in the Java field. I do not understand Steffen's hint about patching prokka. I know that accoding to our web sentinel we prokka is in preparation to be packaged[n1] but patching it for the moment would not have helped. The remark leads to the conclusion that prokka belongs to the preconditions for Mauve. Is this correct? > > For ext/jebl-0.4.jar I'm a bit unsure. Debian contains a package of > > jebl2[6]. I have no idea how to test whether this works as well as > > jebl-0.4. Any hint how to confirm this? > > this is also a package that supports a feature that's still in > development and not enabled in production. It will take me some time to > investigate API changes between jebl and jebl2, so I'd suggest leaving > it out for now. OK, removed from packaging stuff. > > I have created a new Debian package of zeus-jscl. It is in the NEW > > queue and this info page has all its metainformation[7]. It seems that > > the JAR you added to the Mauve download was using a different (probably > > older) zeus-jscl. Thanks to the great Debian community I've git help to > > create a patch against Mauve which adapts the code to the new zeus-jscl > > interface. I would recommend checking out the patch from here[8] and > > take it over to the Mauve code. > > ok, thanks! You are welcome. :-) > > Moreover I noticed that ext/jsc.jar does not seem to be used in Mauve > > at all. Am I right here? This would be really important since if I > > check the download page[9] it says: > > > > Free for non-commercial use. Free educational use is permitted on > > courses where students pay no fees and there are fewer than 40 students. > > Otherwise email Licensing JSC for commercial use. > > > > This would be regarded non-free by Debian and if Mauve would depend from > > this JAR it would not be able to distribute Mauve from main Debian. But > > I think it is fine to simply delete it. Can you please confirm this? > > > > Delete! I'll do this in my repository too. I think there was intention > to use it that never ended up happening. Thats very fortunate since it would have been a potential killer if it would be of some importance. > > My last take is the currently remaining ext/goose.jar. I'm not fully > > sure where I can take the source for this JAR from. Somehow it looks > > like Cereopsis by Dan Tenenbaum but I would like to get your > > confirmation for this first before I'll spent my time into creating a > > package from this project. In any case this would be required to follow > > the Debian policy that we do not allow binary code. So the way is to > > create an appropriate JAR from the source code, create a package from it > > and use this instead of ext/goose.jar (in the same manner as I did for > > zeus-jscl). > > This is from the gaggle project: > http://gaggle.systemsbiology.net/docs/geese/sample/ > yet another feature that's not in production, should be ok to remove. OK, I have deleted it from the packaging in a patch that also removed the file src/org/gel/mauve/gaggle/SampleGoose.java which was referencing the *.jar. > > So far for the JARs. Moreover we would like to run the test suite not > > only to be sure that my JAR replacements were successful. Debian in > > general tries to run any available build time test and has in addition a > > test framework which runs automatically from time to time. Since I have > > seen a test/ directory I wonder how I could trigger the provided tests. > > > > Last but not least I have a problem with your name choice. In Debian we > > just have a package named mauve which is a free test suite for the Java > > Class libraries name[11]. While there is no strong reason to rename the > > binary we are using as wrapper to start Mauve.jar[12] the package name > > has to be changed. (If I remember correctly we discussed this name > > choice back in 2008 - to laze to seek.) In general I do not think that > > it is a good idea to have the same name twice in the Free Software name > > space. > > well, this genome alignment software was first released to the world in > 2003 and development began in 2001, but setting aside the issue of who > came first I think it would be fine to call the package mauve-aligner or > something like that. I am less enthusiastic about renaming the `Mauve` > wrapper script simply to avoid naming conflicts with someone else's > software because that would involve some substantial revision to the > documentation and possibly breaking dependent tools. Hmmm, I think mauve-aligner would be a bad choice if we leave the package containing mauveAligner and progressiveMauve with mauvealigner. The dash as only distinction in the package name sounds a bit weak. What about mauvealigner-gui ? As I said its possible to leave the name "mauve" for the wrapper - possibly also "Mauve" with upper case (please confirm that you prefer the upper case version). > > In any case I would like to discuss the package name where users might > > be able to find Mauve - you might like to point Debian users to this > > package for the simplicity of maintenance and so I'm interested in your > > opinion about the following names: > > > > g-mauve > > genome-mauve > > ? (do you have some better suggestion) > > i think mauve-aligner would be more natural. If you really stick to this would you suggest a different name for the package carrying the command line applications? May be "progressivemauve" aus package name might be a better choice? > > Thanks a lot for taking the time to read this longish mail. Any hints > > and recommendations regarding the packaging are highly appreciated. > > No problem! thanks for taking the time to write such a carefully > considered message!!! I *really* appreciate the effort you are making. > the availability of bio-related debian packages has completely changed > the attitude that biologists i work with take toward linux. you have > taken (most of) the fear out of it. it's wonderful. Thanks for the compliment. However, we would be nothing without you as (cooperative) upstream developers. Kind regards Andreas. > > [1] https://lists.debian.org/debian-med/2008/03/msg00099.html > > [2] > > http://asap.ahabs.wisc.edu/software/software-development-libraries/libgenome.html > > [3] http://sourceforge.net/p/mauve/code/HEAD/tree/libGenome/trunk/ > > [4] https://ftp-master.debian.org/new/mauvealigner_1.2.0+4713-1.html > > [5] > > https://anonscm.debian.org/cgit/debian-med/mauve.git/tree/debian/patches/build_xml.patch > > [6] https://github.com/rambaut/jebl2 > > [7] https://ftp-master.debian.org/new/libzeus-jscl-java_1.72-1.html > > [8] > > https://anonscm.debian.org/cgit/debian-med/mauve.git/tree/debian/patches/use_JConsole_of_zeus-jscl_properly.patch > > [9] http://www.jsc.nildram.co.uk/downloads/download.html > > [10] https://github.com/dtenenbaum/Cereopsis > > [11] http://sourceware.org/mauve/ > > [12] > > https://anonscm.debian.org/cgit/debian-med/mauve.git/tree/debian/bin/mauve [n1] http://blends.debian.org/med/tasks/bio#prokka -- http://fam-tille.de -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". 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