[med-svn] r15952 - in trunk/packages/discosnp/trunk: . debian debian/patches debian/source
Olivier Sallou
osallou at moszumanska.debian.org
Sat Feb 1 11:13:07 UTC 2014
Author: osallou
Date: 2014-02-01 11:13:07 +0000 (Sat, 01 Feb 2014)
New Revision: 15952
Added:
trunk/packages/discosnp/trunk/debian/
trunk/packages/discosnp/trunk/debian/README.debian
trunk/packages/discosnp/trunk/debian/README.source
trunk/packages/discosnp/trunk/debian/changelog
trunk/packages/discosnp/trunk/debian/compat
trunk/packages/discosnp/trunk/debian/control
trunk/packages/discosnp/trunk/debian/copyright
trunk/packages/discosnp/trunk/debian/discosnp.install
trunk/packages/discosnp/trunk/debian/docs
trunk/packages/discosnp/trunk/debian/patches/
trunk/packages/discosnp/trunk/debian/patches/fix_build
trunk/packages/discosnp/trunk/debian/patches/series
trunk/packages/discosnp/trunk/debian/rules
trunk/packages/discosnp/trunk/debian/source/
trunk/packages/discosnp/trunk/debian/source/format
trunk/packages/discosnp/trunk/debian/upstream
trunk/packages/discosnp/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications (1.0.1-1) to trunk
Property changes on: trunk/packages/discosnp/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/discosnp/trunk/debian/README.debian
===================================================================
--- trunk/packages/discosnp/trunk/debian/README.debian (rev 0)
+++ trunk/packages/discosnp/trunk/debian/README.debian 2014-02-01 11:13:07 UTC (rev 15952)
@@ -0,0 +1,12 @@
+discosnp for DEBIAN
+-------------------
+
+No man page is available but to get help, just type: kissreads or kissnp2
+
+Output analysis scripts are:
+ discoSnp_to_genotypes
+ discoSnp_to_cvs
+
+type any on command line to get help.
+
+ -- Olivier Sallou <osallou at debian.org> Mon, 13 Jan 2014 10:55:29 +0100
Added: trunk/packages/discosnp/trunk/debian/README.source
===================================================================
--- trunk/packages/discosnp/trunk/debian/README.source (rev 0)
+++ trunk/packages/discosnp/trunk/debian/README.source 2014-02-01 11:13:07 UTC (rev 15952)
@@ -0,0 +1,7 @@
+There a remaining lintian warning on kissreads.
+Though, we see at compile time that all compilation tags are set.
+
+Could be a false positive:
+
+I: discosnp: hardening-no-fortify-functions usr/bin/kissreads
+
Added: trunk/packages/discosnp/trunk/debian/changelog
===================================================================
--- trunk/packages/discosnp/trunk/debian/changelog (rev 0)
+++ trunk/packages/discosnp/trunk/debian/changelog 2014-02-01 11:13:07 UTC (rev 15952)
@@ -0,0 +1,6 @@
+discosnp (1.0.1-1) UNRELEASED; urgency=medium
+
+ * First debian package (Closes: #737098).
+
+ -- Olivier Sallou <osallou at debian.org> Sat, 01 Feb 2014 16:55:29 +0100
+
Added: trunk/packages/discosnp/trunk/debian/compat
===================================================================
--- trunk/packages/discosnp/trunk/debian/compat (rev 0)
+++ trunk/packages/discosnp/trunk/debian/compat 2014-02-01 11:13:07 UTC (rev 15952)
@@ -0,0 +1 @@
+9
Added: trunk/packages/discosnp/trunk/debian/control
===================================================================
--- trunk/packages/discosnp/trunk/debian/control (rev 0)
+++ trunk/packages/discosnp/trunk/debian/control 2014-02-01 11:13:07 UTC (rev 15952)
@@ -0,0 +1,30 @@
+Source: discosnp
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ bc, zlib1g-dev
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/discosnp/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/discosnp/trunk/
+Homepage: http://colibread.inria.fr/discosnp/
+
+Package: discosnp
+Architecture: any
+Depends: ${misc:Depends}, ${shlibs:Depends},
+ zlib1g, bc, python
+Description: discovering Single Nucleotide Polymorphism from raw set(s) of reads
+ Software discoSnp is designed for discovering Single Nucleotide
+ Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation
+ Sequencers (NGS).
+ .
+ Note that number of input read sets is not constrained, it can be one, two,
+ or more. Note also that no other data as reference genome or annotations
+ are needed.
+ .
+ The software is composed by two modules. First module, kissnp2, detects SNPs
+ from read sets. A second module, kissreads, enhance the kissnp2 results by
+ computing per read set and for each found SNP:
+ 1) its mean read coverage
+ 2) the (phred) quality of reads generating the polymorphism.
Added: trunk/packages/discosnp/trunk/debian/copyright
===================================================================
--- trunk/packages/discosnp/trunk/debian/copyright (rev 0)
+++ trunk/packages/discosnp/trunk/debian/copyright 2014-02-01 11:13:07 UTC (rev 15952)
@@ -0,0 +1,545 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: discosnp
+Source: http://colibread.inria.fr/discosnp/
+
+License: CeCILL
+
+ This Agreement is a free software license that is the result of discussions
+ between its authors in order to ensure compliance with the two main
+ principles guiding its drafting:
+ - firstly, its conformity with French law, both as regards the law of
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+ The following bodies are the authors of this license CeCILL (Ce : CEA, C :
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+ .
+ Commissariat à l'Energie Atomique - CEA, a public scientific, technical and
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+ .
+ .
+ PREAMBLE
+ --------
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+ Article 12 - NEW VERSIONS OF THE AGREEMENT
+ -------------------------------------------
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+ Article 13 - GOVERNING LAW AND JURISDICTION
+ -------------------------------------------
+ .
+ .
+ 13.1. The Agreement is governed by French law. The Parties agree to
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+
+Files: minia/*
+Copyright: 2012 Rayan Chiki <rayan.chikhi at ens-cachan.org>
+ 2012 Guillaume Rizk
+License: CeCILL
+
+Files: *
+Copyright: 2013 INRIA / IRISA
+License: CeCILL
+
+Files: minia/ttmath/*
+Copyright: Tomasz Sowa <t.sowa at ttmath.org>
+License: BSD
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
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+
+
+Files: debian/*
+Copyright: 2013 Olivier Sallou <osallou at debian.org>
+License: GPLv2+
+ The Debian packaging is licensed under the GPL which is available at
+ `/usr/share/common-licenses/GPL'.
+
Added: trunk/packages/discosnp/trunk/debian/discosnp.install
===================================================================
--- trunk/packages/discosnp/trunk/debian/discosnp.install (rev 0)
+++ trunk/packages/discosnp/trunk/debian/discosnp.install 2014-02-01 11:13:07 UTC (rev 15952)
@@ -0,0 +1,5 @@
+output_analyses/discoSnp_to_csv usr/bin/
+output_analyses/discoSnp_to_genotypes usr/bin/
+kissnp2/kissnp2 usr/bin/
+kissreads/kissreads usr/bin/
+data_sample usr/share/doc/discosnp/examples/
Added: trunk/packages/discosnp/trunk/debian/docs
===================================================================
--- trunk/packages/discosnp/trunk/debian/docs (rev 0)
+++ trunk/packages/discosnp/trunk/debian/docs 2014-02-01 11:13:07 UTC (rev 15952)
@@ -0,0 +1 @@
+README.txt
Added: trunk/packages/discosnp/trunk/debian/patches/fix_build
===================================================================
--- trunk/packages/discosnp/trunk/debian/patches/fix_build (rev 0)
+++ trunk/packages/discosnp/trunk/debian/patches/fix_build 2014-02-01 11:13:07 UTC (rev 15952)
@@ -0,0 +1,80 @@
+--- a/kissreads/Makefile
++++ b/kissreads/Makefile
+@@ -19,9 +19,12 @@
+
+ # optimized flags
+
+-CFLAGS=-Wall -O3 -lz -fopenmp
++CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -Wall -O3 -lz
++LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) -Wall -lm -O3 -lz
++
++
+ CFLAGS+=$(MYFLAGS)
+-LDFLAGS+=-Wall -lm -O3 -lz -fopenmp
+
+ ## debug flags
+
+@@ -49,7 +52,7 @@
+ @echo "#################"
+
+ kissreads: $(OBJ)
+- $(CC) -o $@ $^ $(LDFLAGS)
++ $(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
+
+
+ kissReads.o: $(INCLDIR)coherence_algorithm.h $(INCLDIR)couple.h $(INCLDIR)extension_algorithm.h $(INCLDIR)fragment_info.h $(INCLDIR)libchash.h $(INCLDIR)outputs.h $(INCLDIR)commons.h $(INCLDIR)extending_fragment.h $(INCLDIR)fragment_index.h $(INCLDIR)hash.h $(INCLDIR)list.h $(INCLDIR)tree.h
+--- a/minia/makefile
++++ b/minia/makefile
+@@ -1,5 +1,9 @@
+ CC=g++
+-CFLAGS = -O4
++
++CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O4
++LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
++
+ SRC=Pool.cpp Bank.cpp Bloom.cpp Hash16.cpp LargeInt.cpp Kmer.cpp Terminator.cpp Traversal.cpp LinearCounter.cpp Set.cpp Utils.cpp SortingCount.cpp Debloom.cpp OAHash.cpp
+ EXEC=minia
+ OBJ= $(SRC:.cpp=.o)
+@@ -60,7 +64,7 @@
+ all: $(EXEC)
+
+ minia: clean $(OBJ) Minia.cpp
+- $(CC) -o $@ $(OBJ) Minia.cpp $(CFLAGS) -lz
++ $(CC) -o $@ $(OBJ) Minia.cpp $(CFLAGS) $(LDFLAGS) -lz
+
+ %.o: %.cpp %.h
+ $(CC) -o $@ -c $< $(CFLAGS)
+--- a/kissnp2/makefile
++++ b/kissnp2/makefile
+@@ -33,7 +33,10 @@
+ #knowledge of the CeCILL license and that you accept its terms.
+
+ CC=g++
+-CFLAGS= -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
++CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
++LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
++
+ #CFLAGS= -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER -DDONTMARK
+ SRC=../minia/Pool.cpp ../minia/Bank.cpp ../minia/Bloom.cpp ../minia/Hash16.cpp ../minia/Terminator.cpp ../minia/Kmer.cpp ../minia/Traversal.cpp ../minia/LinearCounter.cpp ../minia/Set.cpp ../minia/Utils.cpp ../minia/SortingCount.cpp ../minia/Debloom.cpp ../minia/OAHash.cpp Kmer_for_kissnp2.cpp SNP.cpp filter.cpp IterativeExtensions.cpp commons.cpp
+ EXEC=kissnp2
+@@ -41,7 +44,7 @@
+ all: $(EXEC)
+
+ ifeq ($(prof),1)
+- CFLAGS=-O3 -pg -lz
++ CFLAGS= $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -pg -lz
+ endif
+ ifeq ($(deb),1)
+ CFLAGS+=-O0 -DASSERTS -g -lz
+@@ -79,7 +82,7 @@
+ all: $(EXEC)
+
+ kissnp2: $(OBJ) kissnp2.cpp
+- $(CC) -o $@ $^ $(CFLAGS)
++ $(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
+
+ %.o: %.cpp %.h
+ $(CC) -o $@ -c $< $(CFLAGS)
Added: trunk/packages/discosnp/trunk/debian/patches/series
===================================================================
--- trunk/packages/discosnp/trunk/debian/patches/series (rev 0)
+++ trunk/packages/discosnp/trunk/debian/patches/series 2014-02-01 11:13:07 UTC (rev 15952)
@@ -0,0 +1 @@
+fix_build
Added: trunk/packages/discosnp/trunk/debian/rules
===================================================================
--- trunk/packages/discosnp/trunk/debian/rules (rev 0)
+++ trunk/packages/discosnp/trunk/debian/rules 2014-02-01 11:13:07 UTC (rev 15952)
@@ -0,0 +1,34 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+%:
+ dh $@
+
+get-orig-source:
+ uscan --verbose --force-download --repack --repack-compression xz
+
+override_dh_auto_build:
+ dh_auto_build
+ cd kissnp2 && make k=29
+ cd kissreads && make k=29
+
+override_dh_install:
+ cp output_analyses/discoSnp_to_genotypes.py output_analyses/discoSnp_to_genotypes
+ cp output_analyses/discoSnp_to_csv.py output_analyses/discoSnp_to_csv
+ dh_install
+
+override_dh_clean:
+ cd minia && make clean
+ cd kissnp2 && make clean
+ cd kissreads && make clean
+ rm -f output_analyses/discoSnp_to_genotypes
+ rm -f output_analyses/discoSnp_to_csv
+ rm -f kissnp2/kissnp2
+ rm -f kissreads/kissreads
+ dh_clean
+
+get-orig-source:
+ uscan --verbose --force-download --repack --repack-compression xz
Property changes on: trunk/packages/discosnp/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/discosnp/trunk/debian/source/format
===================================================================
--- trunk/packages/discosnp/trunk/debian/source/format (rev 0)
+++ trunk/packages/discosnp/trunk/debian/source/format 2014-02-01 11:13:07 UTC (rev 15952)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/discosnp/trunk/debian/upstream
===================================================================
--- trunk/packages/discosnp/trunk/debian/upstream (rev 0)
+++ trunk/packages/discosnp/trunk/debian/upstream 2014-02-01 11:13:07 UTC (rev 15952)
@@ -0,0 +1,14 @@
+Homepage: http://minia.genouest.org
+Reference:
+ Author: Chikhi, Rayan and Rizk, Guillaume
+ Title: >
+ Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter.
+ Journal: Algorithms for Molecular Biology
+ Year: 2013
+ Volume: 8
+ Number: 1
+ Pages: 22
+ DOI: 10.1186/1748-7188-8-22
+ PMID: 24040893
+ URL: http://www.almob.org/content/8/1/22
+ eprint: http://minia.genouest.org/files/minia.pdf
Added: trunk/packages/discosnp/trunk/debian/watch
===================================================================
--- trunk/packages/discosnp/trunk/debian/watch (rev 0)
+++ trunk/packages/discosnp/trunk/debian/watch 2014-02-01 11:13:07 UTC (rev 15952)
@@ -0,0 +1,3 @@
+version=3
+
+http://colibread.inria.fr/discosnp/ https://colibread.inria.fr/files/\d+/\d+/discoSnp_([.\d]+)\.zip
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