[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-8-g2e113a6

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 99c8c05231df67ccb037cc6e75a3dd7aee0ca53b
Merge: 1c63e02dccb400fd7cc8e61c4e8783950aafa036 c7c402a1f85d7a9d9726c869dfb0ac36ef594360
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Wed Feb 22 11:01:53 2012 +0100

    Merge branch 'master' of git+ssh://git.debian.org/git/debian-med/bowtie2
    
    Conflicts:
    	debian/rules

diff --combined debian/changelog
index 6afc9ff,4cbb8f2..5d678d6
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,5 -1,5 +1,6 @@@
  bowtie2 (2.0.0-beta5-1) UNRELEASED; urgency=low
  
++  [ Alexandre Mestiashvili ]
    * Initial release (Closes: #660762)
  
-  -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Tue, 21 Feb 2012 18:51:53 +0100
 - -- Alex Mestiashvili <alex at biotec.tu-dresden.de>  Tue, 21 Feb 2012 18:51:53 +0100
++ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Wed, 22 Feb 2012 11:03:03 +0100
diff --combined debian/rules
index 2fa237f,7930ff2..559fce6
--- a/debian/rules
+++ b/debian/rules
@@@ -7,20 -7,15 +7,18 @@@ pkg=$(shell dpkg-parsechangelog | sed -
  
  override_dh_auto_install:
  	mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/
- #	for bin in bowtie2 bowtie2-build bowtie2-inspect bowtie2-align; do \
- #	    help2man $(CURDIR)/$${bin} > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$${bin}.1 ; \
- #	done
 -	for bin in $(pkg) $(pkg)-build $(pkg)-inspect $(pkg)-align; do \
 -	    help2man $(CURDIR)/$${bin} > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$${bin}.1 ; \
 -	done
 -	help2man --name="ultrafast memory-efficient short read aligner" --no-info \
 -             $(CURDIR)/$(pkg) > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$(pkg).1
 -	help2man --name="building a colorspace index for $(pkg)" --no-info \
 -             $(CURDIR)/$(pkg)-build > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$(pkg)-build.1
 -	help2man --name="extracts information from a $(pkg) index" --no-info \
 -             $(CURDIR)/$(pkg)-inspect > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$(pkg)-inspect.1
++
 +	help2man --name="wrapper for bowtie2-align" --no-info \
-              $(CURDIR)/bowtie2 > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie2.1
++	    $(CURDIR)/bowtie2 > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie2.1
 +	help2man --name="builds a Bowtie index from a set of DNA sequences" --no-info \
-              $(CURDIR)/bowtie2-build > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie2-build.1
++	    $(CURDIR)/bowtie2-build > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie2-build.1
 +	help2man --name="extracts information from a bowtie2 index" --no-info \
-              $(CURDIR)/bowtie2-inspect > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie2-inspect.1
++	    $(CURDIR)/bowtie2-inspect > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie2-inspect.1
 +	help2man --name="ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences" --no-info \
-              $(CURDIR)/bowtie2-align> $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie2-align.1
++	    $(CURDIR)/bowtie2-align> $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie2-align.1
 +
 +override_dh_installchangelogs:
-         dh_installchangelogs NEWS
++	dh_installchangelogs NEWS
  
  get-orig-source:
  	. debian/get-orig-source

-- 
ultrafast memory-efficient short read aligner