[Bug 620385] Review Request: BEDTools - A flexible suite of utilities for comparing genomic features

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Mon Aug 2 12:15:05 UTC 2010


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https://bugzilla.redhat.com/show_bug.cgi?id=620385

--- Comment #1 from Adam Huffman <bloch at verdurin.com> 2010-08-02 08:15:04 EDT ---
rpmlint BED*
BEDTools.src:11: W: mixed-use-of-spaces-and-tabs (spaces: line 11, tab: line 1)

- this is the comment relating to the Source URL on Google Code

BEDTools.src: W: invalid-url Source0: BEDTools.v2.8.3.tar.gz

- see above

BEDTools.x86_64: E: script-without-shebang
/usr/share/BEDTools/genomes/mouse.mm8.genome
BEDTools.x86_64: E: script-without-shebang
/usr/share/BEDTools/genomes/human.hg19.genome
BEDTools.x86_64: E: script-without-shebang
/usr/share/BEDTools/genomes/mouse.mm9.genome
BEDTools.x86_64: E: script-without-shebang
/usr/share/BEDTools/genomes/human.hg18.genome
BEDTools.x86_64: E: script-without-shebang
/usr/share/BEDTools/data/rmsk.hg18.chr21.bed
BEDTools.x86_64: E: script-without-shebang
/usr/share/BEDTools/data/knownGene.hg18.chr21.bed

- when I tried to fix these, those two directories took on very strange
permissions, so I'd welcome guidance here
- they're not scripts

BEDTools.x86_64: W: no-manual-page-for-binary complementBed
BEDTools.x86_64: W: no-manual-page-for-binary genomeCoverageBed
BEDTools.x86_64: W: no-manual-page-for-binary mergeBed
BEDTools.x86_64: W: no-manual-page-for-binary pairToPair
BEDTools.x86_64: W: no-manual-page-for-binary groupBy
BEDTools.x86_64: W: no-manual-page-for-binary fastaFromBed
BEDTools.x86_64: W: no-manual-page-for-binary slopBed
BEDTools.x86_64: W: no-manual-page-for-binary bedToIgv
BEDTools.x86_64: W: no-manual-page-for-binary overlap
BEDTools.x86_64: W: no-manual-page-for-binary subtractBed
BEDTools.x86_64: W: no-manual-page-for-binary bamToBed
BEDTools.x86_64: W: no-manual-page-for-binary intersectBed
BEDTools.x86_64: W: no-manual-page-for-binary maskFastaFromBed
BEDTools.x86_64: W: no-manual-page-for-binary bed12ToBed6
BEDTools.x86_64: W: no-manual-page-for-binary bedToBam
BEDTools.x86_64: W: no-manual-page-for-binary sortBed
BEDTools.x86_64: W: no-manual-page-for-binary windowBed
BEDTools.x86_64: W: no-manual-page-for-binary closestBed
BEDTools.x86_64: W: no-manual-page-for-binary linksBed
BEDTools.x86_64: W: no-manual-page-for-binary shuffleBed
BEDTools.x86_64: W: no-manual-page-for-binary coverageBed
BEDTools.x86_64: W: no-manual-page-for-binary pairToBed

- there are no man pages
- I've included the manual file

3 packages and 0 specfiles checked; 6 errors, 24 warnings.

There's also a separate PDF manual at
http://bedtools.googlecode.com/files/BEDTools-User-Manual.v3.pdf - I've
contacted upstream to clarify its licencing.

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