Please stable
looks like seqan cannot be stabilized for months :(, CCus back when arches are CCed there then
Depends on: bug #545154, bug #546816. I think Justin is overloaded. I tried my best in sci overlay, maybe I am wrong but first we need to do something about samtools to avoid the bundled copy (or tophat will install its own samtools_0.1.18 binary + shared lib). Tophat needs certain /usr/bin/samtools binary version (too bad samtools devs did not keep same commadnline switches over the time and even worse, they recycled some for a different purpose). No way it would support newer version easily, especially as tophat_reporter parses SAM output output by the samtools_0.1.18. With seqan requirement it is not that bad, I think we can live with the bundled copy, just headers are need for tophat_reporter and they don't need to be installed. There are no shared/static libs in the seqan package, so no issues here. Somebody please continue from where I left now (sci overlay). commit da3ce5959e5b2a9575a88703a004ed6172e3b31c Author: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> Date: Tue Apr 28 21:04:22 2015 +0200 sci-biology/tophat: recorded depependencies; dropped KEYWORDS until we have slotted samtools (or multiple static binaries with version appended to filename), link tophat_reporter against -lsam-0.1.18 and similarly adjust tophat_reporter
looks like samtools stabilization is blocked :(
sci-biology/tophat is a very brittle package, I'd like to keep it in ~arch in order to be able to fix it quickly.
(In reply to David Seifert from comment #4) > sci-biology/tophat is a very brittle package, I'd like to keep it in ~arch > in order to be able to fix it quickly. Personally I think we should try to stabilize as much packages as possible, I think a -r1 can always live in ~arch. What am I missing David? Don't you have write access to the main portage tree? ;-)
