Red Hat Bugzilla – Bug 708402
Review Request: tophat - A spliced read mapper for RNA-Seq
Last modified: 2016-05-13 08:49:30 EDT
Spec URL: http://verdurin.fedorapeople.org/reviews/tophat/tophat.spec
SRPM URL: http://verdurin.fedorapeople.org/reviews/tophat/tophat-1.2.0-2.fc16.src.rpm
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns
RNA-Seq reads to mammalian-sized genomes using the ultra
high-throughput short read aligner Bowtie, and then analyzes the
mapping results to identify splice junctions between exons.
TopHat is a collaborative effort between the University of Maryland
Center for Bioinformatics and Computational Biology and the University
of California, Berkeley Departments of Mathematics and Molecular and
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 It bundles a newer (though still out of date) version of SeqAn.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.
New bugfix release:
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:
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:
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.