Bug 717473 (SeqAn) - Review Request: SeqAn - Biological sequence analysis library
Summary: Review Request: SeqAn - Biological sequence analysis library
Keywords:
Status: CLOSED DUPLICATE of bug 1105730
Alias: SeqAn
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Nobody's working on this, feel free to take it
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: tophat
TreeView+ depends on / blocked
 
Reported: 2011-06-28 21:39 UTC by Adam Huffman
Modified: 2014-06-24 21:41 UTC (History)
7 users (show)

Fixed In Version:
Doc Type: Bug Fix
Doc Text:
Clone Of:
Environment:
Last Closed: 2013-05-04 14:56:54 UTC


Attachments (Terms of Use)

Description Adam Huffman 2011-06-28 21:39:00 UTC
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
Description: 
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.

Comment 1 Volker Fröhlich 2011-06-28 22:25:32 UTC
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
...

Comment 2 Adam Huffman 2011-06-29 06:58:17 UTC
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...

Comment 3 Volker Fröhlich 2011-06-29 22:41:02 UTC
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 [...]

Comment 4 Adam Huffman 2011-06-29 22:46:39 UTC
Yes, I added that to fix the rpmlint complaint about executable files. Will take a closer look.

Comment 5 Adam Huffman 2012-01-08 12:19:41 UTC
Taking another look at this now.

Comment 6 Adam Huffman 2012-01-30 22:46:06 UTC
Updated to include BR for Boost:

http://verdurin.fedorapeople.org/reviews/SeqAn/SeqAn.spec

http://verdurin.fedorapeople.org/reviews/SeqAn/SeqAn-1.3-5.fc16.src.rpm

Still needs more work.

Comment 7 Volker Fröhlich 2012-02-21 22:35:15 UTC
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
+ ctest
*********************************
No test configuration file found!
*********************************

Comment 8 Volker Fröhlich 2012-05-20 21:33:34 UTC
Adam, are you still working on this package?

Comment 9 Adam Huffman 2012-05-21 08:32:39 UTC
(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.

Comment 10 Sébastien Boisvert 2012-11-03 04:12:06 UTC
So as I understand, there is a confusion regarding the licensing (comment #7). Is that right ?

Comment 11 Volker Fröhlich 2012-11-18 22:13:35 UTC
Not really confusion; the overall license just can't be BSD, because parts of the code are GPL and LGPL of some version.

Comment 12 Volker Fröhlich 2013-05-04 09:43:54 UTC
Adam, what are your plans about SeqAn? If you don't plan to proceed, we can close this ticket.

Comment 13 Adam Huffman 2013-05-04 14:56:54 UTC
No, I'll close this so someone else can take over.

Comment 14 Dave Love 2014-06-06 21:29:28 UTC
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.

http://arc.liv.ac.uk/downloads/misc/SPECS/seqan.spec

Comment 15 Christopher Meng 2014-06-07 02:15:52 UTC

*** This bug has been marked as a duplicate of bug 1105730 ***


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