Re: Microbiomeutil and chimeraslayer as dependency of Qiime
Hi, On Wed, Jun 05, 2013 at 08:34:14AM +0200, "Steffen Möller" wrote: > > microbiomeutil (20101212-2) unstable; urgency=low Done. > We all do not like working with epochs, I presume. I personally do not have a problem with epochs but I respect your feelings. :-) > I would also like to point > to the backports.debian.org page on packaging instructions > at http://backports.debian.org/Contribute/#index5h3 Good hint. I was also wondering whether it is a good idea to use the "ubuntu" string inside BioLinux packages. As a (plain) Ubuntu user I would be a bit confused to see this name in the version if a package is not really part of Ubuntu but just an Ubuntu derivative. So if I were you and I would create versions for BioLinux most probably this would be the best idea for versioning: ~biolinux- or -0biolinux A positive side effect is that people who stumbly by chance about such package will notice the BioLinux string and might become interested in it ... Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130605082541.ga20...@an3as.eu
Re: Microbiomeutil and chimeraslayer as dependency of Qiime
Hi Tim, many thanks for testing! On Wed, Jun 05, 2013 at 12:27:36PM +0100, Tim Booth wrote: > Hi Andreas, > > I spoke too soon on ChimeraSlayer. I've just run the test scripts > provided with QIIME and it is crashing because at some point it tries to > write to the /usr/share/microbiomeutil-data/RESOURCES directory. when I have read until this point I would have considered a patch to write the output to /var/lib/microbiomeutil-data/RESOURCES or even move the whole content to this place. > It looks like this can be fixed by pre-computing some indices, by > running these two commands as root: > > formatdb -p F -i /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta > 2>/dev/null > > cdbfasta -C > /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta I simply trust your experience that this might bethe better solution. > So I guess these commands need to be added to postinst, with a > corresponding cleanup in postrm. Do you know where I can find an > example/template for doing this properly/robustly? When it comes to templates I can only think of /usr/share/debhelper/dh_make/debian > This also hilights that chimeraslayer needs to declare a direct > dependency on the blast2 package. I'd suggest to wait until ftpmaster has accepted the package and reupload then (or file a bug report if somethings stops us in reuploading). I'm not a fan of redrawing and reuploading from / to new queue because it creates extra manual work for ftpmaster which is finally not needed if we fix the problem in SVN quickly and upload a fix soonish. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130605122352.gh20...@an3as.eu
Bug#711212: ITP: libfastutil-java -- Java API providing type-specific maps, sets, lists and queues
Package: wnpp Severity: wishlist Owner: Andreas Tille * Package name: libfastutil-java Version : 6.5.4 Upstream Author : Sebastiano Vigna * URL : http://fastutil.di.unimi.it/ * License : Apache-2.0, LGP Programming Lang: Java Description : Java API providing type-specific maps, sets, lists and queues Fastutil extends the Java™ Collections Framework by providing type-specific maps, sets, lists and queues with a small memory footprint and fast access and insertion; provides also big (64-bit) arrays, sets and lists, and fast, practical I/O classes for binary and text files. . The classes implement their standard counterpart interface (e.g., Map for maps) and can be plugged into existing code. Moreover, they provide additional features (such as bidirectional iterators) that are not available in the standard classes. . Besides objects and primitive types, fastutil classes provide support for references, that is, objects that are compared using the equality operator rather than the equals() method. Remark: I have basically finished the lintian clean packaging and moved the debian/ dir to http://people.debian.org/~tille/packages/libfastutil-java/ In the packaging I used Debian Med team as maintainer which is motivated by the following reasons: 1. It is a precondition for one of the Debian Med targets (goby) as explained here https://lists.debian.org/debian-med/2013/02/msg00152.html 2. If I would stay the only Uploader it would make sense to keep it here because I'm watching this team very closely However, I honestly think that the packaging should rather be done inside the Debian Java team and I'm perfectly fine to move the package in their repository (I can cope with Git and SVN - whatever is prefered). I hope that ACLs are set for DDs so I can commit straight to this dir. Is there any document that describes things I should know about this team. The third option would be to move the package into Debian GIS Project team because my basic motivation to create the package was rather not the precondition for goby but rather to update mkgmap (that's why bug #580170 is in CC). As a last resort I would use collab-maint (which would be the less prefered option for me). What do you think? In any case if you want to become an Uploader of the package and want to share the maintenance that's more than welcome. Kind regards Andreas. -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130605143013.29543.29146.report...@mail.an3as.eu
