Bug 597315 - Review Request: bwa - Burrows-Wheeler Alignment tool
Summary: Review Request: bwa - Burrows-Wheeler Alignment tool
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: Package Review
Version: rawhide
Hardware: All
OS: Linux
medium
medium
Target Milestone: ---
Assignee: Chen Lei
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Keywords:
: 533738 (view as bug list)
Depends On:
Blocks:
TreeView+ depends on / blocked
 
Reported: 2010-05-28 16:02 UTC by Adam Huffman
Modified: 2015-05-30 01:29 UTC (History)
4 users (show)

(edit)
Clone Of:
(edit)
Last Closed: 2010-09-15 05:41:37 UTC
supercyper1: fedora-review+
gwync: fedora-cvs+


Attachments (Terms of Use)

Description Adam Huffman 2010-05-28 16:02:43 UTC
Spec URL: http://verdurin.org.uk/~verdurin/fedora/reviews/bwa/bwa.spec
SRPM URL: http://verdurin.org.uk/~verdurin/fedora/reviews/bwa/bwa-0.5.7-1.fc12.src.rpm
Description: 

BWA is a program for aligning sequencing reads against a large
reference genome (e.g. human genome). It has two major components, one
for reads shorter than 150bp and the other for longer reads.

Comment 1 Chen Lei 2010-05-29 03:52:40 UTC
Some initial comments:

1.Source0 seems not right, I cannot download tarball from this URL.
2. make %{?_smp_mflags} -> make %{?_smp_mflags} CFLAGS="%{optflags}"
You must honor optflags correctly in package.

3.Please also install bwa.1 to %{_mandir}/man1
4.INSTALL should not be included in %doc.

Comment 2 Adam Huffman 2010-05-29 09:52:03 UTC
I've addressed these problems in version 2 - thanks for taking a look so quickly.

Spec URL: http://verdurin.org.uk/~verdurin/fedora/reviews/bwa/bwa.spec
SRPM URL: http://verdurin.org.uk/~verdurin/fedora/reviews/bwa/bwa-0.5.7-2.fc12.src.rpm

rpmlint reports the following warning, which I think can be ignored:

bwa.src: W: spelling-error %description -l en_US bp -> BP, b, p

Comment 3 Chen Lei 2010-05-29 10:25:15 UTC
rpmlint bwa-*
bwa.x86_64: W: spelling-error %description -l en_US bp -> BP, b, p
bwa.x86_64: W: no-manual-page-for-binary qualfa2fq.pl
bwa.x86_64: W: no-manual-page-for-binary solid2fastq.pl
2 packages and 0 specfiles checked; 0 errors, 3 warnings.


Those warings are all harmless, this package is approved .

Comment 4 Adam Huffman 2010-06-06 15:19:20 UTC
New Package CVS Request
=======================
Package Name: bwa
Short Description: Burrows-Wheeler Alignment tool
Owners: verdurin
Branches: F-12 F-13 EL-5
InitialCC:

Comment 5 Kevin Fenzi 2010-06-07 20:59:28 UTC
CVS done (by process-cvs-requests.py).

Do you not want a EL-6 branch as well? File an additional request if you do.

Comment 6 Adam Huffman 2010-06-07 22:47:35 UTC
New Package CVS Request
=======================
Package Name: bwa
Short Description: Burrows-Wheeler Alignment tool
Owners: verdurin
Branches: EL-6
InitialCC:

Comment 7 Kevin Fenzi 2010-06-11 04:50:55 UTC
CVS done.

Comment 8 Fedora Update System 2010-07-12 12:35:07 UTC
bwa-0.5.7-2.fc13 has been submitted as an update for Fedora 13.
http://admin.fedoraproject.org/updates/bwa-0.5.7-2.fc13

Comment 9 Fedora Update System 2010-07-12 12:36:11 UTC
bwa-0.5.7-2.fc12 has been submitted as an update for Fedora 12.
http://admin.fedoraproject.org/updates/bwa-0.5.7-2.fc12

Comment 10 Fedora Update System 2010-07-12 12:46:16 UTC
bwa-0.5.7-2.el5 has been submitted as an update for Fedora EPEL 5.
http://admin.fedoraproject.org/updates/bwa-0.5.7-2.el5

Comment 11 Chen Lei 2010-07-12 14:42:59 UTC
It seems bwa 0.5.8a is out now.

Comment 12 Adam Huffman 2010-07-12 15:20:05 UTC
Indeed - I had neglected to push my builds to Bodhi.  Once I've updated the package, is it best to remove the old update from Bodhi?

Comment 13 Fedora Update System 2010-07-13 07:27:28 UTC
bwa-0.5.7-2.fc12 has been pushed to the Fedora 12 testing repository.  If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing update bwa'.  You can provide feedback for this update here: http://admin.fedoraproject.org/updates/bwa-0.5.7-2.fc12

Comment 14 Fedora Update System 2010-07-13 07:34:41 UTC
bwa-0.5.7-2.fc13 has been pushed to the Fedora 13 testing repository.  If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing update bwa'.  You can provide feedback for this update here: http://admin.fedoraproject.org/updates/bwa-0.5.7-2.fc13

Comment 15 Adam Huffman 2010-07-20 22:45:51 UTC
There is a compilation problem with 0.5.8a - I'll submit a new update once I've fixed it.

Comment 16 Fedora Update System 2010-07-21 12:24:43 UTC
bwa-0.5.7-2.el5 has been pushed to the Fedora EPEL 5 testing repository.  If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing update bwa'.  You can provide feedback for this update here: http://admin.fedoraproject.org/updates/bwa-0.5.7-2.el5

Comment 17 Fedora Update System 2010-08-05 10:54:10 UTC
bwa-0.5.8a-1.fc13 has been submitted as an update for Fedora 13.
http://admin.fedoraproject.org/updates/bwa-0.5.8a-1.fc13

Comment 18 Fedora Update System 2010-08-05 10:55:17 UTC
bwa-0.5.8a-1.fc12 has been submitted as an update for Fedora 12.
http://admin.fedoraproject.org/updates/bwa-0.5.8a-1.fc12

Comment 19 Fedora Update System 2010-08-05 10:56:11 UTC
bwa-0.5.8a-1.el5 has been submitted as an update for Fedora EPEL 5.
http://admin.fedoraproject.org/updates/bwa-0.5.8a-1.el5

Comment 20 Fedora Update System 2010-08-05 23:28:10 UTC
bwa-0.5.8a-1.fc12 has been pushed to the Fedora 12 testing repository.  If problems still persist, please make note of it in this bug report.
 If you want to test the update, you can install it with 
 su -c 'yum --enablerepo=updates-testing update bwa'.  You can provide feedback for this update here: http://admin.fedoraproject.org/updates/bwa-0.5.8a-1.fc12

Comment 21 Martin Gieseking 2010-08-24 08:10:20 UTC
*** Bug 533738 has been marked as a duplicate of this bug. ***

Comment 22 Fedora Update System 2010-09-14 17:30:07 UTC
bwa-0.5.8a-1.el5 has been pushed to the Fedora EPEL 5 stable repository.  If problems still persist, please make note of it in this bug report.

Comment 23 Fedora Update System 2010-09-15 05:25:35 UTC
bwa-0.5.8a-1.fc13 has been pushed to the Fedora 13 stable repository.  If problems still persist, please make note of it in this bug report.

Comment 24 Fedora Update System 2010-09-15 05:41:32 UTC
bwa-0.5.8a-1.fc12 has been pushed to the Fedora 12 stable repository.  If problems still persist, please make note of it in this bug report.

Comment 25 Adam Huffman 2015-05-29 21:49:18 UTC
Package Change Request
======================
Package Name: bwa
New Branches: EL-7
Owners: verdurin

Comment 26 Gwyn Ciesla 2015-05-30 01:29:05 UTC
Git done (by process-git-requests).


Note You need to log in before you can comment on or make changes to this bug.