| Summary: | sci-biology/tophat-2.1.1-r1 and sci-biology/samtools-0.1.20-r2 please stabilize | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Justin Lecher (RETIRED) <jlec> |
| Component: | [OLD] Keywording and Stabilization | Assignee: | Gentoo Science Biology related packages <sci-biology> |
| Status: | RESOLVED OBSOLETE | ||
| Severity: | enhancement | CC: | mmokrejs |
| Priority: | Normal | Keywords: | STABLEREQ |
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Bug Depends on: | 525628, 577854 | ||
| Bug Blocks: | |||
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Description
Justin Lecher (RETIRED)
2014-10-17 07:53:33 UTC
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? ;-) |