[med-svn] [rna-star] 01/05: new upstream release

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository rna-star.

commit 85a82fa10eb47d53120bafc604a34b9166ef07d9
Author: Sascha Steinbiss <satta at debian.org>
Date:   Fri Jan 26 13:24:43 2018 +0100

    new upstream release
---
 debian/STAR.1                            |  4 ++--
 debian/changelog                         |  2 +-
 debian/patches/donotuse_own_htslib.patch | 16 ++++++++--------
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/debian/STAR.1 b/debian/STAR.1
index a385067..4c345f6 100644
--- a/debian/STAR.1
+++ b/debian/STAR.1
@@ -1,4 +1,4 @@
-.TH STAR "1" "January 2015" "STAR 2.4.0i" "User Commands"
+.TH STAR "1" "January 2018" "STAR 2.5.4a" "User Commands"
 .SH NAME
 STAR \- ultrafast universal RNA-seq aligner
 .SH DESCRIPTION
@@ -19,7 +19,7 @@ junctions with an 80-90% success rate, corroborating the high precision
 of the STAR mapping strategy.
 .SH SYNOPSIS
 .B STAR
-\fB--option1-name option1-value(s)--option2-name option2-value(s) ...\fR
+\fB[options]... --genomeDir REFERENCE --readFilesIn R1.fq R2.fq\fR
 .SH SEE ALSO
 This manpage is only a placeholder.  You can get extensive information
 by using
diff --git a/debian/changelog b/debian/changelog
index c0ac587..030bd45 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-rna-star (2.5.4a+dfsg-1) UNRELEASED; urgency=medium
+rna-star (2.5.4a+dfsg-1) unstable; urgency=medium
 
   [ Sascha Steinbiss ]
   * New upstream release.
diff --git a/debian/patches/donotuse_own_htslib.patch b/debian/patches/donotuse_own_htslib.patch
index 2eeb604..65422a8 100644
--- a/debian/patches/donotuse_own_htslib.patch
+++ b/debian/patches/donotuse_own_htslib.patch
@@ -4,7 +4,7 @@ Description: Use Debian packaged htslib
 
 --- a/source/Makefile
 +++ b/source/Makefile
-@@ -12,17 +12,17 @@ CXXFLAGSextra ?=
+@@ -12,17 +12,17 @@
  CXX ?= g++
  
  # pre-defined flags
@@ -28,7 +28,7 @@ Description: Use Debian packaged htslib
  
  CFLAGS := -O3 -pipe -Wall -Wextra $(CFLAGS)
  
-@@ -54,10 +54,10 @@ SOURCES := $(wildcard *.cpp) $(wildcard
+@@ -54,10 +54,10 @@
  
  
  %.o : %.cpp
@@ -41,7 +41,7 @@ Description: Use Debian packaged htslib
  
  all: STAR
  
-@@ -68,12 +68,10 @@ clean:
+@@ -68,12 +68,10 @@
  .PHONY: CLEAN
  CLEAN:
  	rm -f *.o STAR Depend.list
@@ -54,16 +54,16 @@ Description: Use Debian packaged htslib
  
  .PHONY: install
  install:
-@@ -84,7 +82,7 @@ ifneq ($(MAKECMDGOALS),cleanRelease)
+@@ -84,7 +82,7 @@
  ifneq ($(MAKECMDGOALS),CLEAN)
  ifneq ($(MAKECMDGOALS),STARforMac)
  ifneq ($(MAKECMDGOALS),STARforMacGDB)
 -Depend.list: $(SOURCES) parametersDefault.xxd htslib
 +Depend.list: $(SOURCES) parametersDefault.xxd
  	echo $(SOURCES)
- 	/bin/rm -f ./Depend.list
+ 	'rm' -f ./Depend.list
  	$(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
-@@ -95,11 +93,6 @@ endif
+@@ -95,11 +93,6 @@
  endif
  endif
  
@@ -88,7 +88,7 @@ Description: Use Debian packaged htslib
  #include "ErrorWarning.h"
 --- a/source/bam_cat.c
 +++ b/source/bam_cat.c
-@@ -52,8 +52,8 @@ THE SOFTWARE.
+@@ -52,8 +52,8 @@
  #include <stdlib.h>
  #include <unistd.h>
  
@@ -133,7 +133,7 @@ Description: Use Debian packaged htslib
  //    kstring_t strK;
 --- a/source/STAR.cpp
 +++ b/source/STAR.cpp
-@@ -26,7 +26,7 @@
+@@ -27,7 +27,7 @@
  #include "sjdbInsertJunctions.h"
  #include "bam_cat.h"
  

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