[med-svn] r18620 - in trunk/packages: . rna-star rna-star/trunk rna-star/trunk/debian rna-star/trunk/debian/patches rna-star/trunk/debian/source
Steffen Möller
moeller at moszumanska.debian.org
Thu Jan 29 11:39:35 UTC 2015
Author: moeller
Date: 2015-01-29 11:39:34 +0000 (Thu, 29 Jan 2015)
New Revision: 18620
Added:
trunk/packages/rna-star/
trunk/packages/rna-star/trunk/
trunk/packages/rna-star/trunk/debian/
trunk/packages/rna-star/trunk/debian/README.Debian
trunk/packages/rna-star/trunk/debian/README.source
trunk/packages/rna-star/trunk/debian/changelog
trunk/packages/rna-star/trunk/debian/compat
trunk/packages/rna-star/trunk/debian/control
trunk/packages/rna-star/trunk/debian/copyright
trunk/packages/rna-star/trunk/debian/docs
trunk/packages/rna-star/trunk/debian/files
trunk/packages/rna-star/trunk/debian/install
trunk/packages/rna-star/trunk/debian/patches/
trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch
trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch
trunk/packages/rna-star/trunk/debian/patches/series
trunk/packages/rna-star/trunk/debian/rules
trunk/packages/rna-star/trunk/debian/source/
trunk/packages/rna-star/trunk/debian/source/format
Log:
The tool STAR (rna-star) works for me
It would be nice to find someone who really cares
about this package.
Added: trunk/packages/rna-star/trunk/debian/README.Debian
===================================================================
--- trunk/packages/rna-star/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/rna-star/trunk/debian/README.Debian 2015-01-29 11:39:34 UTC (rev 18620)
@@ -0,0 +1,10 @@
+rna-star for Debian
+-------------------
+
+The packaging is not completed. Please adopt.
+
+The package name reflects the project name
+with Google Code - just "star" was considered
+too ambiguous.
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 28 Jan 2015 18:15:51 +0100
Added: trunk/packages/rna-star/trunk/debian/README.source
===================================================================
--- trunk/packages/rna-star/trunk/debian/README.source (rev 0)
+++ trunk/packages/rna-star/trunk/debian/README.source 2015-01-29 11:39:34 UTC (rev 18620)
@@ -0,0 +1,9 @@
+star for Debian
+---------------
+
+ * removed all binaries with rm bin/*/STAR
+ * removed source/htslib
+ * removed .gitignore
+
+
+
Added: trunk/packages/rna-star/trunk/debian/changelog
===================================================================
--- trunk/packages/rna-star/trunk/debian/changelog (rev 0)
+++ trunk/packages/rna-star/trunk/debian/changelog 2015-01-29 11:39:34 UTC (rev 18620)
@@ -0,0 +1,5 @@
+rna-star (2.4.0i-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 28 Jan 2015 18:15:51 +0100
Added: trunk/packages/rna-star/trunk/debian/compat
===================================================================
--- trunk/packages/rna-star/trunk/debian/compat (rev 0)
+++ trunk/packages/rna-star/trunk/debian/compat 2015-01-29 11:39:34 UTC (rev 18620)
@@ -0,0 +1 @@
+8
Added: trunk/packages/rna-star/trunk/debian/control
===================================================================
--- trunk/packages/rna-star/trunk/debian/control (rev 0)
+++ trunk/packages/rna-star/trunk/debian/control 2015-01-29 11:39:34 UTC (rev 18620)
@@ -0,0 +1,19 @@
+Source: rna-star
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 8.0.0), libhts-dev
+Standards-Version: 3.9.6
+Homepage: https://code.google.com/p/rna-star/
+#Vcs-Git: git://git.debian.org/collab-maint/star.git
+#Vcs-Browser: http://git.debian.org/?p=collab-maint/star.git;a=summary
+
+Package: rna-star
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Spliced Transcripts Alignment to a Reference
+ STAR is an ultrafast universal RNA-seq aligner.
+ .
+ A. Dobin et al, Bioinformatics 2012;
+ doi: 10.1093/bioinformatics/bts635
+ http://bioinformatics.oxfordjournals.org/content/29/1/15
Added: trunk/packages/rna-star/trunk/debian/copyright
===================================================================
--- trunk/packages/rna-star/trunk/debian/copyright (rev 0)
+++ trunk/packages/rna-star/trunk/debian/copyright 2015-01-29 11:39:34 UTC (rev 18620)
@@ -0,0 +1,38 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: star
+Source: <url://example.com>
+
+Files: *
+Copyright: <years> <put author's name and email here>
+ <years> <likewise for another author>
+License: <special license>
+ <Put the license of the package here indented by 1 space>
+ <This follows the format of Description: lines in control file>
+ .
+ <Including paragraphs>
+
+# If you want to use GPL v2 or later for the /debian/* files use
+# the following clauses, or change it to suit. Delete these two lines
+Files: debian/*
+Copyright: 2015 Steffen Moeller <moeller at debian.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
+# Please avoid to pick license terms that are more restrictive than the
+# packaged work, as it may make Debian's contributions unacceptable upstream.
Added: trunk/packages/rna-star/trunk/debian/docs
===================================================================
--- trunk/packages/rna-star/trunk/debian/docs (rev 0)
+++ trunk/packages/rna-star/trunk/debian/docs 2015-01-29 11:39:34 UTC (rev 18620)
@@ -0,0 +1 @@
+README
Added: trunk/packages/rna-star/trunk/debian/files
===================================================================
--- trunk/packages/rna-star/trunk/debian/files (rev 0)
+++ trunk/packages/rna-star/trunk/debian/files 2015-01-29 11:39:34 UTC (rev 18620)
@@ -0,0 +1 @@
+star_2.4.0i-1_amd64.deb science optional
Added: trunk/packages/rna-star/trunk/debian/install
===================================================================
Added: trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch
===================================================================
--- trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch (rev 0)
+++ trunk/packages/rna-star/trunk/debian/patches/compilationstuff.patch 2015-01-29 11:39:34 UTC (rev 18620)
@@ -0,0 +1,69 @@
+Index: star-2.4.0i/source/Parameters.h
+===================================================================
+--- star-2.4.0i.orig/source/Parameters.h
++++ star-2.4.0i/source/Parameters.h
+@@ -54,7 +54,7 @@
+ int readFilesIndex;
+ uint32 readFilesN;
+ vector <string> readFilesIn, readFilesInTmp;
+- vector <vector <string>> readFilesNames;
++ vector <vector <string> > readFilesNames;
+ uint readNmates;
+ string readMatesLengthsIn;
+ vector <string> readFilesCommand;
+Index: star-2.4.0i/source/Makefile
+===================================================================
+--- star-2.4.0i.orig/source/Makefile
++++ star-2.4.0i/source/Makefile
+@@ -17,28 +17,28 @@
+ bam_cat.o
+ SOURCES := $(wildcard *.cpp) $(wildcard *.c)
+
+-LDFLAGS := -pthread -Bstatic -lhts -Bdynamic -lz
+-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
+-LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
+-LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
++LDFLAGS += -pthread -lhts -lz
++LDFLAGS_static += -static -static-libgcc -pthread -Lhtslib -lhts -lz
++LDFLAGS_Mac +=-pthread -lz htslib/libhts.a
++LDFLAGS_Mac_static +=-pthread -lz -static-libgcc htslib/libhts.a
+
+-LDFLAGS_gdb := $(LDFLAGS)
++LDFLAGS_gdb += $(LDFLAGS)
+
+ COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'
+ EXTRAFLAGS :=
+
+-CCFLAGS_common := -pipe -std=c++0x -Wall -Wextra -fopenmp $(COMPTIMEPLACE) $(OPTIMFLAGS) $(OPTIMFLAGS1) $(EXTRAFLAGS)
+-CCFLAGS_main := -O3 $(CCFLAGS_common)
+-CCFLAGS_gdb := -O0 -g $(CCFLAGS_common)
++CCFLAGS_common += -pipe -std=c++0x -Wall -Wextra -fopenmp $(COMPTIMEPLACE) $(OPTIMFLAGS) $(OPTIMFLAGS1) $(EXTRAFLAGS)
++CCFLAGS_main += -O3 $(CCFLAGS_common)
++CCFLAGS_gdb += -O0 -g $(CCFLAGS_common)
+
+ CXX :=g++
+
+
+ %.o : %.cpp
+- $(CXX) -c $(CCFLAGS) $<
++ $(CXX) -c $(CCFLAGS) $(COMPTIMEPLACE) $<
+
+ %.o : %.c
+- $(CXX) -c $(CCFLAGS) $<
++ $(CXX) -c $(CCFLAGS) $(COMPTIMEPLACE) $<
+
+ all: STAR
+
+Index: star-2.4.0i/source/STAR.cpp
+===================================================================
+--- star-2.4.0i.orig/source/STAR.cpp
++++ star-2.4.0i/source/STAR.cpp
+@@ -314,7 +314,7 @@
+ vector <string> bamBinNamesV;
+ for (uint32 ibin=0; ibin<RAchunk[0]->chunkOutBAMcoord->nBins; ibin++) {
+
+- bamBinNamesV.push_back(P->outBAMsortTmpDir+"/b"+to_string((uint) ibin));
++ bamBinNamesV.push_back(P->outBAMsortTmpDir+"/b"+std::to_string((uint) ibin));
+ struct stat buffer;
+ if (stat (bamBinNamesV.back().c_str(), &buffer) != 0) {//check if file exists
+ bamBinNamesV.pop_back();
Added: trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch
===================================================================
--- trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch (rev 0)
+++ trunk/packages/rna-star/trunk/debian/patches/donotuse_own_htslib.patch 2015-01-29 11:39:34 UTC (rev 18620)
@@ -0,0 +1,100 @@
+Index: star-2.4.0i/source/Makefile
+===================================================================
+--- star-2.4.0i.orig/source/Makefile
++++ star-2.4.0i/source/Makefile
+@@ -17,7 +17,7 @@
+ bam_cat.o
+ SOURCES := $(wildcard *.cpp) $(wildcard *.c)
+
+-LDFLAGS := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
++LDFLAGS := -pthread -Bstatic -lhts -Bdynamic -lz
+ LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
+ LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
+ LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
+@@ -49,20 +49,17 @@
+ .PHONY: CLEAN
+ CLEAN:
+ rm -f *.o STAR Depend.list
+- $(MAKE) -C htslib clean
+
+ .PHONY: cleanRelease
+ cleanRelease:
+ rm -f *.o Depend.list
+- $(MAKE) -C htslib clean
+-
+
+ ifneq ($(MAKECMDGOALS),clean)
+ ifneq ($(MAKECMDGOALS),cleanRelease)
+ ifneq ($(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
+ $(CXX) $(CCFLAGS_common) -MM $^ >> Depend.list
+@@ -73,11 +70,6 @@
+ endif
+ endif
+
+-htslib : htslib/libhts.a
+-
+-htslib/libhts.a :
+- $(MAKE) -C htslib lib-static
+-
+ parametersDefault.xxd: parametersDefault
+ xxd -i parametersDefault > parametersDefault.xxd
+
+Index: star-2.4.0i/source/STAR.cpp
+===================================================================
+--- star-2.4.0i.orig/source/STAR.cpp
++++ star-2.4.0i/source/STAR.cpp
+@@ -22,7 +22,7 @@
+ #include "mapThreadsSpawn.h"
+ #include "ErrorWarning.h"
+
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+ extern int bam_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outbam);
+
+ int main(int argInN, char* argIn[]) {
+Index: star-2.4.0i/source/bamRemoveDuplicates.cpp
+===================================================================
+--- star-2.4.0i.orig/source/bamRemoveDuplicates.cpp
++++ star-2.4.0i/source/bamRemoveDuplicates.cpp
+@@ -1,7 +1,7 @@
+ #include <unordered_map>
+ #include "bamRemoveDuplicates.h"
+ #include <iostream>
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+ #include "IncludeDefine.h"
+ #include SAMTOOLS_BGZF_H
+ #include "ErrorWarning.h"
+Index: star-2.4.0i/source/bam_cat.c
+===================================================================
+--- star-2.4.0i.orig/source/bam_cat.c
++++ star-2.4.0i/source/bam_cat.c
+@@ -49,8 +49,8 @@
+ #include <stdlib.h>
+ #include <unistd.h>
+
+-#include "htslib/htslib/bgzf.h"
+-#include "htslib/htslib/sam.h"
++#include <htslib/bgzf.h>
++#include <htslib/sam.h>
+ #include <cstring>
+
+ #define BUF_SIZE 0x10000
+Index: star-2.4.0i/source/signalFromBAM.h
+===================================================================
+--- star-2.4.0i.orig/source/signalFromBAM.h
++++ star-2.4.0i/source/signalFromBAM.h
+@@ -1,6 +1,6 @@
+ #ifndef CODE_signalFromBAM
+ #define CODE_signalFromBAM
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+ #include <fstream>
+ #include <string>
+ #include "Stats.h"
Added: trunk/packages/rna-star/trunk/debian/patches/series
===================================================================
--- trunk/packages/rna-star/trunk/debian/patches/series (rev 0)
+++ trunk/packages/rna-star/trunk/debian/patches/series 2015-01-29 11:39:34 UTC (rev 18620)
@@ -0,0 +1,2 @@
+donotuse_own_htslib.patch
+compilationstuff.patch
Added: trunk/packages/rna-star/trunk/debian/rules
===================================================================
--- trunk/packages/rna-star/trunk/debian/rules (rev 0)
+++ trunk/packages/rna-star/trunk/debian/rules 2015-01-29 11:39:34 UTC (rev 18620)
@@ -0,0 +1,30 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/buildflags.mk
+
+export CCFLAGS=-flto $(CXXFLAGS) $(CPPFLAGS) -std=c++0x
+export LDFLAGS+=-flto -pthread -lhts -lz
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ cd source && $(MAKE) CCFLAGS_common=-flto CCFLAGS="$(CCFLAGS)" LDFLAGS="$(LDFLAGS)"
+
+override_dh_auto_install:
+ mkdir -p debian/star/usr/bin/
+ cp source/STAR debian/star/usr/bin/
+
+
+override_dh_auto_clean:
+ cd source && $(MAKE) clean
Property changes on: trunk/packages/rna-star/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/rna-star/trunk/debian/source/format
===================================================================
--- trunk/packages/rna-star/trunk/debian/source/format (rev 0)
+++ trunk/packages/rna-star/trunk/debian/source/format 2015-01-29 11:39:34 UTC (rev 18620)
@@ -0,0 +1 @@
+3.0 (quilt)
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