Bug 708402 (tophat)
| Summary: | Review Request: tophat - A spliced read mapper for RNA-Seq | ||
|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | Adam Huffman <bloch> |
| Component: | Package Review | Assignee: | Nobody's working on this, feel free to take it <nobody> |
| Status: | CLOSED NOTABUG | QA Contact: | Fedora Extras Quality Assurance <extras-qa> |
| Severity: | medium | Docs Contact: | |
| Priority: | medium | ||
| Version: | rawhide | CC: | alex, dave.love, fedora-package-review, ron, volker27 |
| Target Milestone: | --- | Keywords: | Reopened |
| Target Release: | --- | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Fixed In Version: | Doc Type: | Bug Fix | |
| Doc Text: | Story Points: | --- | |
| Clone Of: | Environment: | ||
| Last Closed: | 2020-08-09 00:45:51 UTC | Type: | --- |
| Regression: | --- | Mount Type: | --- |
| Documentation: | --- | CRM: | |
| Verified Versions: | Category: | --- | |
| oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |
| Cloudforms Team: | --- | Target Upstream Version: | |
| Embargoed: | |||
| Bug Depends On: | 717473, 1105730 | ||
| Bug Blocks: | 201449 | ||
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Description
Adam Huffman
2011-05-27 14:48:50 UTC
This package bundles an old version of SeqAn (http://www.seqan.de/). Please separately package this library and delete it in the prep section before building then. Ugh. I've made a start on SeqAn and that bundles an old copy of samtools... Anyway, I'll make a separate review request for that. 1.3.0 is now out. It bundles a newer (though still out of date) version of SeqAn. I'll try contacting the upstream authors about this, though they haven't responded to any of my other queries so far. http://verdurin.fedorapeople.org/reviews/tophat/tophat.spec http://verdurin.fedorapeople.org/reviews/tophat/tophat-1.3.0-1.fc16.src.rpm New bugfix release: http://verdurin.fedorapeople.org/reviews/tophat/tophat.spec http://verdurin.fedorapeople.org/reviews/tophat/tophat-1.3.1-1.fc14.src.rpm I'll post my SeqAn request shortly. SeqAn request is at https://bugzilla.redhat.com/show_bug.cgi?id=717473 Update to 1.3.3: http://verdurin.fedorapeople.org/reviews/tophat/tophat.spec http://verdurin.fedorapeople.org/reviews/tophat/tophat-1.3.3-1.fc16.src.rpm SeqAn must still be un-bundled from tophat to finish the review. Yes, I'm looking at SeqAn again now. Still working on SeqAn. In the meantime, updated to 1.4.0: http://verdurin.fedorapeople.org/reviews/tophat/tophat.spec http://verdurin.fedorapeople.org/reviews/tophat/tophat-1.4.0-1.fc16.src.rpm I'll update this in light of the recent 2.0.x releases and submit SeqAn separately. A pity there's so much bundling in these applications. Closing since SeqAn was closed WONTFIX. seqan is packaged. There's a tophat build currently under https://copr.fedoraproject.org/coprs/loveshack/livhpc/build/83875/. It requires an unbundled tinythread++ from the same copr, which I could submit if it helps this go through. Unfortunately it can't currently go in EPEL6, due to the boost version required, but it's in the above copr using the boost scl if anyone wants it. (In reply to Dave Love from comment #12) > Unfortunately it can't currently go in EPEL6, > due to the boost version required, but it's in the above copr using the > boost scl if anyone wants it. Oops, I forgot that seqan is missing from EPEL and won't build in copr, probably due to memory usage. The srpm does work if you can build your own seqan. For what it's worth, http://www.ccb.jhu.edu/software/tophat/index.shtml now says tophat is "largely superseded". There's a quick go at hisat2, the replacement, in the above copr; it hasn't been tested, though. This is an automatic check from review-stats script. This review request ticket hasn't been updated for some time. We're sorry it is taking so long. If you're still interested in packaging this software into Fedora repositories, please respond to this comment clearing the NEEDINFO flag. You may want to update the specfile and the src.rpm to the latest version available and to propose a review swap on Fedora devel mailing list to increase chances to have your package reviewed. If this is your first package and you need a sponsor, you may want to post some informal reviews. Read more at https://fedoraproject.org/wiki/How_to_get_sponsored_into_the_packager_group. Without any reply, this request will shortly be considered abandoned and will be closed. Thank you for your patience. This is an automatic action taken by review-stats script. The ticket submitter failed to clear the NEEDINFO flag in a month. As per https://fedoraproject.org/wiki/Policy_for_stalled_package_reviews we consider this ticket as DEADREVIEW and proceed to close it. |