Bug 716400

Summary:	Review Request: MACS - Model-based Analysis for ChIP-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 WONTFIX	QA Contact:	Fedora Extras Quality Assurance <extras-qa>
Severity:	medium	Docs Contact:
Priority:	medium
Version:	rawhide	CC:	fedora-package-review, tomspur, volker27
Target Milestone:	---
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Hardware:	All
OS:	Linux
Whiteboard:
Fixed In Version:		Doc Type:	Bug Fix
Doc Text:		Story Points:	---
Clone Of:		Environment:
Last Closed:	2014-07-01 14:02:20 UTC	Type:	---
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Verified Versions:		Category:	---
oVirt Team:	---	RHEL 7.3 requirements from Atomic Host:
Cloudforms Team:	---	Target Upstream Version:

Description Adam Huffman 2011-06-24 10:15:51 UTC

Spec URL: http://verdurin.fedorapeople.org/reviews/MACS/MACS.spec
SRPM URL: http://verdurin.fedorapeople.org/reviews/MACS/MACS-1.4.0-1.fc16.src.rpm
Description: 

Next generation parallel sequencing technologies made chromatin
immunoprecipitation followed by sequencing (ChIP-Seq) a popular
strategy to study genome-wide protein-DNA interactions, while creating
challenges for analysis algorithms. We present Model-based Analysis of
ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer
(Illumina / Solexa). MACS empirically models the length of the
sequenced ChIP fragments, which tends to be shorter than sonication or
library construction size estimates, and uses it to improve the
spatial resolution of predicted binding sites. MACS also uses a
dynamic Poisson distribution to effectively capture local biases in
the genome sequence, allowing for more sensitive and robust
prediction. MACS compares favorably to existing ChIP-Seq peak-finding
algorithms, is publicly available open source, and can be used for
ChIP-Seq with or without control samples.

Comment 1 Adam Huffman 2011-06-29 22:25:30 UTC

Update for 1.4.1 release:

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

http://verdurin.fedorapeople.org/reviews/MACS/MACS-1.4.1-1.fc16.src.rpm

Comment 2 Volker Fröhlich 2011-08-30 06:48:06 UTC

I suggest to ask the developers to put their releases in a more standard directory, like %{name}-%{version}, or at least remove the hash from its name.

You might want to use this if clause:

http://fedoraproject.org/wiki/Packaging:Python#Macros

macs.1* should probably be macs.1.*

You could be a bit more specific in the files section, stating something like:

%{python_sitelib}/%{name}*
%{python_sitelib}/%{name}-%{version}-py*.egg

Comment 3 Thomas Spura 2011-10-09 12:57:37 UTC

Any news here?

Comment 4 Adam Huffman 2011-10-09 16:32:55 UTC

New version addressing the issues in https://bugzilla.redhat.com/show_bug.cgi?id=716400#c2 at:

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

http://verdurin.fedorapeople.org/reviews/MACS/MACS-1.4.1-2.fc17.src.rpm

While I want to have EPEL5/6 branches, I don't like too many conditionals, so I've made a separate branch in Git for Fedora vs. EPEL.  The version up for review is the Fedora one.

Comment 5 Volker Fröhlich 2012-03-07 16:44:44 UTC

The version you uploaded still has all the elements necessary for EPEL5. I'd recommend NOT to maintain separate spec file, since the obsolete elements don't hurt. They're just not useful if you packaged for Fedora only.

Please preserve the timestamp of the manpage by adding -p to the install command.

defattr is not necessary (since EPEL4).

"macs.1* should probably be macs.1.*" -- I must apologize on this one: Your version was perfectly fine and mine is not.

Comment 6 Adam Huffman 2014-07-01 14:02:20 UTC

I haven't been working in this field for over two years now, so it would be better for someone else to maintain this package, if there is interest.