[med-svn] r1755 - in trunk/packages/ncbi-epcr/trunk/debian: . patches
tille at alioth.debian.org
tille at alioth.debian.org
Mon Apr 14 13:56:05 UTC 2008
Author: tille
Date: 2008-04-14 13:56:05 +0000 (Mon, 14 Apr 2008)
New Revision: 1755
Added:
trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.install
trunk/packages/ncbi-epcr/trunk/debian/patches/10_assert.patch
Removed:
trunk/packages/ncbi-epcr/trunk/debian/README
trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr-data.dirs
trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.dirs
trunk/packages/ncbi-epcr/trunk/debian/patches/01_Makefiles.patch
Modified:
trunk/packages/ncbi-epcr/trunk/debian/changelog
trunk/packages/ncbi-epcr/trunk/debian/control
trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.docs
trunk/packages/ncbi-epcr/trunk/debian/patches/series
trunk/packages/ncbi-epcr/trunk/debian/rules
Log:
Packaging for latest e-PCR; completely different from previous packaging, because no
data that would need an extra data package; more binaries (man pages not yet written);
PLEASE TEST
Deleted: trunk/packages/ncbi-epcr/trunk/debian/README
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/README 2008-04-14 07:54:22 UTC (rev 1754)
+++ trunk/packages/ncbi-epcr/trunk/debian/README 2008-04-14 13:56:05 UTC (rev 1755)
@@ -1,87 +0,0 @@
-================================================================
-Electronic PCR (e-PCR) program for finding STSs in DNA sequences
-================================================================
-
-REFERENCE: G.D.Schuler. Sequence mapping by Electronic PCR.
- Genome Research 7: 541-550, 1997.
-
-FEEDBACK: schuler at ncbi.nlm.nih.gov
-
-USAGE: e-PCR <stsfile> <seqfile>
-
- Where <stsfile> is one of the files in the db directory or
- one that you supply (see below for format specification)
- and <seqfile> is a FASTA-style file containing any number
- of sequences.
-
-
-SYSTEMS SUPPORTED
-=================
-Sun Solaris 5.9/Sparc
-Sun Solaris 5.9/x86
-Linux/i386 (glibc-2.2.4)
-
-
-INSTALLATION
-============
-Just identify the correct executable for your system and copy to a
-location that is on the search path. You can use any of the following
-commands to test the program; they should all produce some output.
-
- e-PCR db/genethon.sts samples/L78833.nt
-
- e-PCR db/genethon.sts samples/U47924.nt
-
- e-PCR db/txmap.sts samples/U47924.nt
-
-
-STS DATABASE FILES
-==================
-genethon.sts Genethon genetic markers (Dib et al, 1996)
-txmap.sts Transcript Map markers (Schuler et al, 1996)
-
-
-STS DATABASE FILE SPECIFICATION
-===============================
-The stsfile should contain at least four (optionally five)
-tab-delimited columns:
-
-col-1: STS name
-col-2: left PCR primer
-col-3: right PCR primer
-col-4: PCR product size
-col-5: (optional) additional text to be included in the output
-
-
-PACKING LIST
-============
-
-./README
-
-./bin/sunos-sparc/e-PCR
-./bin/sunos-intel/e-PCR
-./bin/linux-intel/e-PCR
-
-./db/dbsts.sts
-./db/genethon.sts
-./db/txmap.sts
-
-./samples/L78833.nt
-./samples/U47924.nt
-
-./src/e-PCR.cpp
-./src/fasta-io.cpp
-./src/fasta-io.h
-./src/Makefile
-./src/stsmatch.cpp
-./src/stsmatch.h
-./src/util.cpp
-./src/util.h
-./src/gdsutil.cpp
-./src/gdsutil.h
-./src/version.h
-
-
-THANKS
-======
-Serge Batalov
Modified: trunk/packages/ncbi-epcr/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/changelog 2008-04-14 07:54:22 UTC (rev 1754)
+++ trunk/packages/ncbi-epcr/trunk/debian/changelog 2008-04-14 13:56:05 UTC (rev 1755)
@@ -1,5 +1,9 @@
-epcr (1.2.0-4) unstable; urgency=low
+epcr (2.3.9-1) unstable; urgency=low
+ * New upstream version
+ #385256
+ There are no reasonable files targetting at a ncbi-epcr-data package
+ and thus this is dropped
* Group maintenance by Debian-Med team
- DM-Upload-Allowed: Yes
- Vcs tags
@@ -10,8 +14,9 @@
* Standards-Version: 3.7.3 (no changes needed)
* debhelper >= 5
* Patches using quilt
+ * Use cdbs
- -- Andreas Tille <tille at debian.org> Tue, 08 Apr 2008 15:50:46 +0200
+ -- Andreas Tille <tille at debian.org> Mon, 14 Apr 2008 13:13:05 +0200
epcr (1.2.0-3) unstable; urgency=low
* Added patch for compilation on Alpha (presumably)
Modified: trunk/packages/ncbi-epcr/trunk/debian/control
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/control 2008-04-14 07:54:22 UTC (rev 1754)
+++ trunk/packages/ncbi-epcr/trunk/debian/control 2008-04-14 13:56:05 UTC (rev 1755)
@@ -5,7 +5,7 @@
DM-Upload-Allowed: yes
Uploaders: Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 5.0), docbook-to-man, quilt
+Build-Depends: debhelper (>= 5.0), docbook-to-man, quilt, cdbs
Standards-Version: 3.7.3
Homepage: http://www.ncbi.nlm.nih.gov/sutils/e-pcr/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ncbi-epcr/trunk/?rev=0&sc=0
@@ -14,7 +14,7 @@
Package: ncbi-epcr
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: bioperl, ncbi-epcr-data
+Recommends: bioperl
Description: Tool to test a DNA sequence for the presence of sequence tagged sites
Electronic PCR feature to test a DNA sequence for the presence of
sequence tagged sites. e-PCR looks for STSs in DNA sequences by
@@ -22,15 +22,3 @@
the correct order, orientation, and spacing that they could plausibly
prime the amplification of a PCR product of the correct molecular weight
(Schuler, Genome Research 7:541-50, 1997).
-
-
-Package: ncbi-epcr-data
-Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: ncbi-epcr
-Description: NCBI public STS data
- Databases with marker data.
- .
- dbsts.sts
- genethon.sts
- txmap.sts
Deleted: trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr-data.dirs
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr-data.dirs 2008-04-14 07:54:22 UTC (rev 1754)
+++ trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr-data.dirs 2008-04-14 13:56:05 UTC (rev 1755)
@@ -1,4 +0,0 @@
-usr/share/ncbi
-usr/share/ncbi/e-PCR
-usr/share/ncbi/e-PCR/db
-usr/share/ncbi/e-PCR/samples
Deleted: trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.dirs
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.dirs 2008-04-14 07:54:22 UTC (rev 1754)
+++ trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.dirs 2008-04-14 13:56:05 UTC (rev 1755)
@@ -1 +0,0 @@
-usr/bin
Modified: trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.docs
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.docs 2008-04-14 07:54:22 UTC (rev 1754)
+++ trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.docs 2008-04-14 13:56:05 UTC (rev 1755)
@@ -1 +1,3 @@
-debian/README
+README.txt
+README.html
+
Added: trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.install
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.install (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.install 2008-04-14 13:56:05 UTC (rev 1755)
@@ -0,0 +1,4 @@
+e-PCR usr/bin
+famap usr/bin
+fahash usr/bin
+re-PCR usr/bin
Deleted: trunk/packages/ncbi-epcr/trunk/debian/patches/01_Makefiles.patch
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/patches/01_Makefiles.patch 2008-04-14 07:54:22 UTC (rev 1754)
+++ trunk/packages/ncbi-epcr/trunk/debian/patches/01_Makefiles.patch 2008-04-14 13:56:05 UTC (rev 1755)
@@ -1,72 +0,0 @@
---- e-pcr-1.2.0.orig.orig/Makefile
-+++ e-pcr-1.2.0.orig/Makefile
-@@ -1,11 +1,16 @@
-+DESTDIR=""
-
- .PHONY: all install clean
-
- all:
- (cd src && $(MAKE) all)
-
--install:
-+
-+DBPATH=$(DESTDIR)-data/usr/share/ncbi/e-PCR
-+install: all
- (cd src && $(MAKE) install)
-+ mkdir -p $(DBPATH)/db && cp db/* $(DBPATH)/db
-+ mkdir -p $(DBPATH)/samples && cp samples/* $(DBPATH)/samples
-
- clean:
-- (cd src && $(MAKE) clean)
-+ (cd src && $(MAKE) clean-all )
---- e-pcr-1.2.0.orig.orig/src/Makefile
-+++ e-pcr-1.2.0.orig/src/Makefile
-@@ -1,5 +1,11 @@
- srcdir = .
--USR_BINDIR = ../bin/
-+DESTDIR=""
-+ifeq ($(DESTDIR),"")
-+ USR_BINDIR = ../bin/
-+else
-+ USR_BINDIR = $(DESTDIR)/usr/bin
-+endif
-+
-
- FLAGS =
-
-@@ -7,7 +13,8 @@
- # GNU compiler flags
- CC = gcc
- CXX = g++
--CXXFLAGS = -O2 -I. $(FLAGS) -I$(USR_INCDIR) `getconf LFS_CFLAGS`
-+CXXFLAGS = -O2 -I. $(FLAGS) `getconf LFS_CFLAGS`
-+#CXXFLAGS = -O2 -I. $(FLAGS) -I$(USR_INCDIR) `getconf LFS_CFLAGS`
- LDFLAGS = `getconf LFS_LDFLAGS` `getconf LFS_LIBS` -L. -lseq
-
- #########################################################################
-@@ -22,7 +29,7 @@
-
-
- $(USR_BINDIR)/% : %
-- -ln -f $@ $@%
-+ -ln -f $@ $@% || true
- install -s $< $(USR_BINDIR)
-
- TEST_BINARIES = \
-@@ -39,13 +46,13 @@
-
-
- clean:
-- -rm *.o
-+ -rm -f *.o
-
- clean-all: clean
-- -rm libseq.a $(TEST_BINARIES)
-+ -rm -f libseq.a $(TEST_BINARIES)
-
- dist-clean: clean-all
-- -rm *~
-+ -rm -f *~
-
- libseq.a : $(OBJFILES)
- - rm -f libseq.a
Added: trunk/packages/ncbi-epcr/trunk/debian/patches/10_assert.patch
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/patches/10_assert.patch (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/patches/10_assert.patch 2008-04-14 13:56:05 UTC (rev 1755)
@@ -0,0 +1,10 @@
+--- e-PCR-2.3.9.orig/e-PCR_main.cpp
++++ e-PCR-2.3.9/e-PCR_main.cpp
+@@ -32,6 +32,7 @@
+
+ #include <epcr/stsmatch.hpp>
+
++#include <assert.h>
+ #include <errno.h>
+ #include <time.h>
+
Modified: trunk/packages/ncbi-epcr/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/patches/series 2008-04-14 07:54:22 UTC (rev 1754)
+++ trunk/packages/ncbi-epcr/trunk/debian/patches/series 2008-04-14 13:56:05 UTC (rev 1755)
@@ -1 +1 @@
-01_Makefiles.patch
+10_assert.patch
Modified: trunk/packages/ncbi-epcr/trunk/debian/rules
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/rules 2008-04-14 07:54:22 UTC (rev 1754)
+++ trunk/packages/ncbi-epcr/trunk/debian/rules 2008-04-14 13:56:05 UTC (rev 1755)
@@ -1,95 +1,21 @@
#!/usr/bin/make -f
-# debian/rules for clustalw-mpi
-# Copyright 2004-2008 Steffen Moeller, Andreas Tille
-# GPL
+# debian/rules for ncbi-epcr using cdbs
+# Andreas Tille <tille at debian.org>, GPL
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
-include /usr/share/quilt/quilt.make
+DEB_MAKE_CLEAN_TARGET := clean
+clean::
+ rm -f epcr
+ rm -f libepcr.a
+ rm -f e-PCR famap fahash re-PCR
+ rm -f debian/e-PCR.1
-CFLAGS = -Wall -g
+DEB_OPT_FLAG += -I. -g2 -DDEALLOCATE=0 `getconf LFS_CFLAGS` -DVERSION=\\\"2.3.9\\\" -DVER_MAJOR=2 -DVER_MINOR=3 -DVER_BUILD=9 -DSTANDALONE=1
-ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
- CFLAGS += -O0
-else
- CFLAGS += -O2
-endif
-ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
- INSTALL_PROGRAM += -s
-endif
+LDFLAGS += `getconf LFS_LDFLAGS` `getconf LFS_LIBS` -L.
-configure: configure-stamp
-configure-stamp:
- dh_testdir
- # Add here commands to configure the package.
-
- touch configure-stamp
-
-build: patch build-stamp
-
-build-stamp: configure-stamp
- dh_testdir
-
- $(MAKE)
+build/ncbi-epcr::
/usr/bin/docbook-to-man debian/e-PCR.sgml > debian/e-PCR.1
-
- touch build-stamp
-
-clean-patched:
- dh_testdir
- dh_testroot
- rm -f build-stamp configure-stamp
-
- $(MAKE) clean
-
- dh_clean debian/e-PCR.1
-
-clean: clean-patched unpatch
-
-install: build
- dh_testdir
- dh_testroot
- dh_clean -k
- dh_installdirs
-
- $(MAKE) install DESTDIR=$(CURDIR)/debian/ncbi-epcr
-
-
-# Build architecture-independent files here.
-binary-indep: build install
-# We have nothing to do by default.
-
-# Build architecture-dependent files here.
-binary-arch: build install
- dh_testdir
- dh_testroot
- dh_installchangelogs
- dh_installdocs
- dh_installexamples
-# dh_install
-# dh_installmenu
-# dh_installdebconf
-# dh_installlogrotate
-# dh_installemacsen
-# dh_installpam
-# dh_installmime
-# dh_installinit
-# dh_installcron
-# dh_installinfo
- dh_installman
- dh_link
- dh_strip
- dh_compress
- dh_fixperms
-# dh_perl
-# dh_python
-# dh_makeshlibs
- dh_installdeb
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure
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