Red Hat Bugzilla – Bug 717473
Review Request: SeqAn - Biological sequence analysis library
Last modified: 2014-06-24 17:41:52 EDT
Spec URL: http://verdurin.fedorapeople.org/reviews/SeqAn/SeqAn.spec
SRPM URL: http://verdurin.fedorapeople.org/reviews/SeqAn/SeqAn-1.3-4.fc15.src.rpm
SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological
data. Our library applies a unique generic design that guarantees high
performance, generality, extensibility, and integration with other
libraries. SeqAn is easy to use and simplifies the development of new
software tools with a minimal loss of performance.
Rabema and Stellar are licensed as GPLv3+, other components are LGPLv3+.
Did you manage to use the system wide samtools?
The package doesn't build in Mock or with rpmbuild: rm: cannot remove `SeqAn-1.3/apps/stellar/examples/reads.fasta': Permission denied
Thanks for looking - it definitely needs more work, I just wanted to start the process.
Puzzled by the error as it builds fine in Mock for me (for F15 - for some reason it complains about not being able to find samtools-devel on F14).
There's also a question of naming. Upstream they oscillate between SeqAn, Seqan and seqan...
The tests aren't executed.
I found out, what causes my build troubles:
+ rm -rf SeqAn-1.3
rm: cannot remove `SeqAn-1.3/apps/stellar/examples/reads.fasta': Permission denied
rm: cannot remove `SeqAn-1.3/apps/stellar/examples/NC_001477.fasta': Permission denied
rm: cannot remove `SeqAn-1.3/apps/stellar/examples/NC_001474.fasta': Permission denied
The examples directory ends up with 644, although it isn't like that in the tarball. I happens while installing:
+ chmod 0644 /builddir/build/BUILD/SeqAn-1.3/apps/stellar/README /builddir/build/BUILD/SeqAn-1.3/apps/stellar/examples [...]
Yes, I added that to fix the rpmlint complaint about executable files. Will take a closer look.
Taking another look at this now.
Updated to include BR for Boost:
Still needs more work.
You can remove defattr. By stating Python >= 2.5, you excluded EPEL 5 and can therefore remove clean section, rm in install section and buildroot definition too.
I fail to see where the library is. If there is no library, the devel package doesn't make any sense, as far as I know.
The license file should be in the main package.
Repeating for completeness' sake: Parts of this package are GPL and LGPL. The overall license can not be BSD therefore.
The trouble from comment #3 is still there, by the way.
The tests don't seem to run:
+ cd /builddir/build/BUILD
+ cd SeqAn-1.3
+ unset DISPLAY
No test configuration file found!
Adam, are you still working on this package?
(In reply to comment #8)
> Adam, are you still working on this package?
Haven't looked at it in a while. I've changed jobs now and am no longer in the biology field, so this is less of a personal priority. However, if people do want it, I'm happy to try and complete the initial packaging.
So as I understand, there is a confusion regarding the licensing (comment #7). Is that right ?
Not really confusion; the overall license just can't be BSD, because parts of the code are GPL and LGPL of some version.
Adam, what are your plans about SeqAn? If you don't plan to proceed, we can close this ticket.
No, I'll close this so someone else can take over.
I've worked on this. Presumably it will need a new review request, and I'll have
to check the build of tophat against it, which may take me a while, but I thought it
was worth recording that it's in progress.
*** This bug has been marked as a duplicate of bug 1105730 ***