[med-svn] r1708 - in trunk/packages: . ncbi-epcr ncbi-epcr/trunk ncbi-epcr/trunk/debian ncbi-epcr/trunk/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Tue Apr 8 13:44:07 UTC 2008
Author: tille
Date: 2008-04-08 13:44:06 +0000 (Tue, 08 Apr 2008)
New Revision: 1708
Added:
trunk/packages/ncbi-epcr/
trunk/packages/ncbi-epcr/tags/
trunk/packages/ncbi-epcr/trunk/
trunk/packages/ncbi-epcr/trunk/debian/
trunk/packages/ncbi-epcr/trunk/debian/README
trunk/packages/ncbi-epcr/trunk/debian/README.Debian
trunk/packages/ncbi-epcr/trunk/debian/changelog
trunk/packages/ncbi-epcr/trunk/debian/compat
trunk/packages/ncbi-epcr/trunk/debian/control
trunk/packages/ncbi-epcr/trunk/debian/copyright
trunk/packages/ncbi-epcr/trunk/debian/e-PCR.sgml
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/ncbi-epcr.docs
trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.manpages
trunk/packages/ncbi-epcr/trunk/debian/patches/
trunk/packages/ncbi-epcr/trunk/debian/patches/01_Makefiles.patch
trunk/packages/ncbi-epcr/trunk/debian/patches/series
trunk/packages/ncbi-epcr/trunk/debian/rules
Log:
Initial check in of ncbi-epcr with debian/patches instread of patched files
Added: trunk/packages/ncbi-epcr/trunk/debian/README
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/README (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/README 2008-04-08 13:44:06 UTC (rev 1708)
@@ -0,0 +1,87 @@
+================================================================
+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
Added: trunk/packages/ncbi-epcr/trunk/debian/README.Debian
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/README.Debian 2008-04-08 13:44:06 UTC (rev 1708)
@@ -0,0 +1,13 @@
+e-pcr for Debian
+----------------
+
+The data was separated in the package ncbi-epcr-data from the main program.
+
+As a scientist please remember to cite
+ Gregory D. Schuler
+ Sequence Mapping by Electronic PCR
+ Genome Research 7:541-550
+when using this program and consider to inform the author at
+schuler at ncbi.nlm.nih.gov on such citations.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>, Thu, 20 Nov 2003 12:50:19 +0100
Added: trunk/packages/ncbi-epcr/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/changelog (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/changelog 2008-04-08 13:44:06 UTC (rev 1708)
@@ -0,0 +1,20 @@
+epcr (1.2.0-3) unstable; urgency=low
+ * Added patch for compilation on Alpha (presumably)
+ and IA64 (patch by Sebastian Muszynski, thanks
+ also go to Lamont Jones) (Closes: #239733).
+ * data package is now architecture-independent (Closes: #233421).
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Thu, 20 Feb 2004 12:50:19 +0100
+epcr (1.2.0-2) unstable; urgency=low
+
+ * Corrected structure of man page
+ * Reduced number of ignored errors during build process to
+ ease automated interpretation of buildd logs
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Thu, 20 Feb 2004 12:50:19 +0100
+epcr (1.2.0-1) unstable; urgency=low
+
+ * Initial Release (Closes:#221847).
+ * Separated samples and databases to -data package
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Thu, 20 Nov 2003 12:50:19 +0100
+
Added: trunk/packages/ncbi-epcr/trunk/debian/compat
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/compat (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/compat 2008-04-08 13:44:06 UTC (rev 1708)
@@ -0,0 +1 @@
+4
Added: trunk/packages/ncbi-epcr/trunk/debian/control
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/control (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/control 2008-04-08 13:44:06 UTC (rev 1708)
@@ -0,0 +1,33 @@
+Source: epcr
+Section: science
+Priority: extra
+Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>
+Build-Depends: debhelper (>= 4.0.0), docbook-to-man
+Standards-Version: 3.6.1
+
+Package: ncbi-epcr
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: bioperl, ncbi-epcr-data
+Description: [Biology] 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
+ searching for subsequences that closely match the PCR primers and have
+ 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).
+ .
+ Homepage: http://www.ncbi.nlm.nih.gov/genome/sts/epcr.cgi
+
+Package: ncbi-epcr-data
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: ncbi-epcr
+Description: [Biology] NCBI public STS data
+ Databases with marker data.
+ .
+ dbsts.sts
+ genethon.sts
+ txmap.sts
+ .
+ Homepage: http://www.ncbi.nlm.nih.gov/genome/sts/epcr.cgi
Added: trunk/packages/ncbi-epcr/trunk/debian/copyright
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/copyright (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/copyright 2008-04-08 13:44:06 UTC (rev 1708)
@@ -0,0 +1,32 @@
+This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
+Thu, 20 Nov 2003 12:50:19 +0100.
+
+It was downloaded from ftp://ftp.ncbi.nih.gov/pub/schuler
+
+Upstream Authors: Gregory D. Schuler <schuler at ncbi.nlm.nih.gov>
+
+Copyright:
+
+Public domain. No particular license. To quote an email the upstream author sent:
+
+"
+Steffen,
+
+I don't know what Debian is, but the e-PCR code is
+in the public domain, so anyone can do anything
+with it.
+
+Cheers,
+-greg
+"
+
+As this license apparently passes the
+
+ Island test
+
+ Dissident test
+
+ and the "tentacles of evil" test
+
+(http://people.debian.org/~bap/dfsg-faq.html) this program is considered
+to be DFSGL conform.
Added: trunk/packages/ncbi-epcr/trunk/debian/e-PCR.sgml
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/e-PCR.sgml (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/e-PCR.sgml 2008-04-08 13:44:06 UTC (rev 1708)
@@ -0,0 +1,146 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+<!-- Process this file with docbook-to-man to generate an nroff manual
+ page: `docbook-to-man manpage.sgml > manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>FIRSTNAME</firstname>">
+ <!ENTITY dhsurname "<surname>SURNAME</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>November 20, 2003</date>">
+ <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+ allowed: see man(7), man(1). -->
+ <!ENTITY dhsection "<manvolnum>SECTION</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>E-PCR</refentrytitle>">
+ <!ENTITY dhpackage "e-PCR">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>Find sequence tagged sites (STS) in DNA sequences</refpurpose>
+ </refnamediv>
+
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage; stsfile seqfile</command>
+
+ <arg><option><replaceable>options</replaceable></option></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+ <para>
+ The program substitutes blast in the location of pairs primers on the genome that may yield a PCR product.
+ </para>
+ </refsect1>
+ <refsect1>
+ <title>OPTIONS</title>
+ <para>
+ </para>
+ <variablelist>
+ <varlistentry>
+ <term><option>M=<replaceable>##</replaceable></option>
+ </term>
+ <listitem>
+ <para>Margin (default 50)</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>N=<replaceable>##</replaceable></option>
+ </term>
+ <listitem>
+ <para>Number of mismatches allowed (default 0)</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-mid</option>
+ </term>
+ <listitem>
+ <para>Show midpoint of STS location instead of range</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+
+ <para>bioperl (1)</para>
+ <para>/usr/share/doc/ncbi-epcr</para>
+ <para>/usr/share/ncbi/e-PCR/db/<sequence tag data> in ncbi-epcr-data</para>
+ <para>/usr/share/ncbi/e-PCR/samples/<sequences from genbank> in ncbi-epcr-data</para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+ </para>
+ <para>
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+ </para>
+
+ </refsect1>
+</refentry>
+
+<!-- Keep this comment at the end of the file
+Local variables:
+mode: sgml
+sgml-omittag:t
+sgml-shorttag:t
+sgml-minimize-attributes:nil
+sgml-always-quote-attributes:t
+sgml-indent-step:2
+sgml-indent-data:t
+sgml-parent-document:nil
+sgml-default-dtd-file:nil
+sgml-exposed-tags:nil
+sgml-local-catalogs:nil
+sgml-local-ecat-files:nil
+End:
+-->
+
+
Added: trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr-data.dirs
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr-data.dirs (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr-data.dirs 2008-04-08 13:44:06 UTC (rev 1708)
@@ -0,0 +1,4 @@
+usr/share/ncbi
+usr/share/ncbi/e-PCR
+usr/share/ncbi/e-PCR/db
+usr/share/ncbi/e-PCR/samples
Added: trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.dirs
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.dirs (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.dirs 2008-04-08 13:44:06 UTC (rev 1708)
@@ -0,0 +1 @@
+usr/bin
Added: trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.docs
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.docs (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.docs 2008-04-08 13:44:06 UTC (rev 1708)
@@ -0,0 +1 @@
+README
Added: trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.manpages
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.manpages (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/ncbi-epcr.manpages 2008-04-08 13:44:06 UTC (rev 1708)
@@ -0,0 +1 @@
+debian/e-PCR.1
Added: trunk/packages/ncbi-epcr/trunk/debian/patches/01_Makefiles.patch
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/patches/01_Makefiles.patch (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/patches/01_Makefiles.patch 2008-04-08 13:44:06 UTC (rev 1708)
@@ -0,0 +1,72 @@
+--- 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)/sample && 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 : $(OBJFILES)
+ - rm -f libseq.a
Added: trunk/packages/ncbi-epcr/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/patches/series (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/patches/series 2008-04-08 13:44:06 UTC (rev 1708)
@@ -0,0 +1 @@
+01_Makefiles.patch
Added: trunk/packages/ncbi-epcr/trunk/debian/rules
===================================================================
--- trunk/packages/ncbi-epcr/trunk/debian/rules (rev 0)
+++ trunk/packages/ncbi-epcr/trunk/debian/rules 2008-04-08 13:44:06 UTC (rev 1708)
@@ -0,0 +1,94 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# GNU copyright 1997 to 1999 by Joey Hess.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
+ INSTALL_PROGRAM += -s
+endif
+
+configure: configure-stamp
+configure-stamp:
+ dh_testdir
+ # Add here commands to configure the package.
+
+ touch configure-stamp
+
+build: build-stamp
+
+build-stamp: configure-stamp
+ dh_testdir
+
+ # Add here commands to compile the package.
+ $(MAKE)
+ /usr/bin/docbook-to-man debian/e-PCR.sgml > debian/e-PCR.1
+
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp
+
+ # Add here commands to clean up after the build process.
+ -$(MAKE) clean
+
+ dh_clean debian/e-PCR.1
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+ # Add here commands to install the package into debian/e-pcr.
+ $(MAKE) install DESTDIR=$(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
Property changes on: trunk/packages/ncbi-epcr/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
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