[med-svn] r98 - in trunk/packages/primer3/trunk: . debian src test
Charles Plessy
charles-guest at costa.debian.org
Wed Aug 23 14:53:21 UTC 2006
Author: charles-guest
Date: 2006-08-23 14:53:19 +0000 (Wed, 23 Aug 2006)
New Revision: 98
Added:
trunk/packages/primer3/trunk/debian/
trunk/packages/primer3/trunk/debian/README.Debian
trunk/packages/primer3/trunk/debian/changelog
trunk/packages/primer3/trunk/debian/compat
trunk/packages/primer3/trunk/debian/control
trunk/packages/primer3/trunk/debian/copyright
trunk/packages/primer3/trunk/debian/dirs
trunk/packages/primer3/trunk/debian/docs
trunk/packages/primer3/trunk/debian/install
trunk/packages/primer3/trunk/debian/manpages
trunk/packages/primer3/trunk/debian/rules
trunk/packages/primer3/trunk/primer3.sgml
Modified:
trunk/packages/primer3/trunk/src/Makefile
trunk/packages/primer3/trunk/test/dpal_gen.pl
trunk/packages/primer3/trunk/test/dpal_test.pl
trunk/packages/primer3/trunk/test/long_seq_tm_test.pl
trunk/packages/primer3/trunk/test/primer_test.pl
Log:
Load primer3-1.0.0 into trunk/packages/primer3/trunk.
Added: trunk/packages/primer3/trunk/debian/README.Debian
===================================================================
--- trunk/packages/primer3/trunk/debian/README.Debian 2006-08-23 14:43:00 UTC (rev 97)
+++ trunk/packages/primer3/trunk/debian/README.Debian 2006-08-23 14:53:19 UTC (rev 98)
@@ -0,0 +1,15 @@
+primer3 for Debian
+-----------------
+
+The cgi interface was deliberately not put into /usr/lib/cgi-bin for an
+increased security. The files are kept in /usr/share/doc/primer3.
+
+The authors agrees to a distribution of Primer3 in Debian. However,
+he does not see a chance to change the license to a free license. The
+current license requires the copyright of the MIT Whitehead institute to
+be stated next to the product name whenever Primer3 is announced and the
+copyright holder claims the right to forbid such a distribution. This
+is not compatible with a distribution of Primer3 in the main section
+of debian.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>, Wed, 31 Mar 2004 15:07:10 +0200
Added: trunk/packages/primer3/trunk/debian/changelog
===================================================================
--- trunk/packages/primer3/trunk/debian/changelog 2006-08-23 14:43:00 UTC (rev 97)
+++ trunk/packages/primer3/trunk/debian/changelog 2006-08-23 14:53:19 UTC (rev 98)
@@ -0,0 +1,22 @@
+primer3 (1.0.0-1) unstable; urgency=low
+
+ * Initial release. (Closes: #241235)
+ * 4-clause BSD licences are DFSG-free, change of section to main/optional.
+ * Swiching to collaborative maintainance: Maintainer is a mailing-list,
+ Uploaders are real people.
+ * Using debhelper v5.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 23 Aug 2006 22:06:24 +0900
+
+primer3 (0.9-0.2) unstable; urgency=low
+
+ * Contacted upstream author, change of section to non-free/optional.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Wed, 1 Apr 2004 15:07:10 +0200
+
+primer3 (0.9-0.1) unstable; urgency=low
+
+ * Pre-Release.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Wed, 31 Mar 2004 15:07:10 +0200
+
Added: trunk/packages/primer3/trunk/debian/compat
===================================================================
--- trunk/packages/primer3/trunk/debian/compat 2006-08-23 14:43:00 UTC (rev 97)
+++ trunk/packages/primer3/trunk/debian/compat 2006-08-23 14:53:19 UTC (rev 98)
@@ -0,0 +1 @@
+5
Added: trunk/packages/primer3/trunk/debian/control
===================================================================
--- trunk/packages/primer3/trunk/debian/control 2006-08-23 14:43:00 UTC (rev 97)
+++ trunk/packages/primer3/trunk/debian/control 2006-08-23 14:53:19 UTC (rev 98)
@@ -0,0 +1,28 @@
+Source: primer3
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <steffen_moeller at gmx.de>, Charles Plessy <charles-debian-nospam at plessy.org>
+Build-Depends: debhelper (>= 5), docbook-to-man
+Standards-Version: 3.7.2
+
+Package: primer3
+Architecture: any
+Depends:
+Recommends: libcgi-perl, apache | httpd
+Suggests: ncbi-epcr
+Description: [Biology] Tool to design flanking oligo nucleotides for DNA amplification
+ Primer3 picks primers for PCR reactions, considering as criteria
+ oligonucleotide melting temperature, size, GC content and primer-dimer
+ possibilities, PCR product size, positional constraints within the source
+ sequence, and miscellaneous other constraints. All of these criteria are
+ user-specifiable as constraints, and some are specifiable as terms in an
+ objective function that characterizes an optimal primer pair.
+ .
+ It has been published in Rozen S and Skaletsky H, "Primer3 on the WWW for
+ general users and for biologist programmers.", Methods Mol Biol. 2000;132:365-86.
+ .
+ The Whitehead Institute for Biomedical Research provides a web-based
+ front end to Primer3.
+ .
+ Homepage: http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi
Added: trunk/packages/primer3/trunk/debian/copyright
===================================================================
--- trunk/packages/primer3/trunk/debian/copyright 2006-08-23 14:43:00 UTC (rev 97)
+++ trunk/packages/primer3/trunk/debian/copyright 2006-08-23 14:53:19 UTC (rev 98)
@@ -0,0 +1,54 @@
+This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
+Wed, 31 Mar 2004 15:07:10 +0200.
+
+It was downloaded from: http://www-genome.wi.mit.edu/genome_software/other/primer3.html
+
+Upstream Authors: Steve Rozen <steve at wi.mit.edu>, Helen J. Skaletsky
+
+Copyright:
+
+ Copyright (c) 1996,1997,1998,1999,2000,2001,2004
+ Whitehead Institute for Biomedical Research. All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions must reproduce the above copyright notice, this
+list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution. Redistributions of
+source code must also reproduce this information in the source code itself.
+
+2. If the program is modified, redistributions must include a notice
+(in the same places as above) indicating that the redistributed program is
+not identical to the version distributed by Whitehead Institute.
+
+3. All advertising materials mentioning features or use of this
+software must display the following acknowledgment:
+ This product includes software developed by the
+ Whitehead Institute for Biomedical Research.
+
+4. The name of the Whitehead Institute may not be used to endorse or
+promote products derived from this software without specific prior written
+permission.
+
+We also request that use of this software be cited in publications as
+
+ Rozen, S., Skaletsky, H. "Primer3 on the WWW for general
+ users and for biologist programmers." In S. Krawetz and
+ S. Misener, eds. Bioinformatics Methods and Protocols in
+ the series Methods in Molecular Biology. Humana Press,
+ Totowa, NJ, 2000, pages 365-386. Code available at
+ http://fokker.wi.mit.edu/primer3/
+
+
+THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ``AS IS'' AND ANY
+EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE WHITEHEAD INSTITUTE BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGE.
Added: trunk/packages/primer3/trunk/debian/dirs
===================================================================
--- trunk/packages/primer3/trunk/debian/dirs 2006-08-23 14:43:00 UTC (rev 97)
+++ trunk/packages/primer3/trunk/debian/dirs 2006-08-23 14:53:19 UTC (rev 98)
@@ -0,0 +1,3 @@
+usr/bin
+usr/lib/cgi-bin
+var/www
Added: trunk/packages/primer3/trunk/debian/docs
===================================================================
--- trunk/packages/primer3/trunk/debian/docs 2006-08-23 14:43:00 UTC (rev 97)
+++ trunk/packages/primer3/trunk/debian/docs 2006-08-23 14:53:19 UTC (rev 98)
@@ -0,0 +1,2 @@
+README
+src/release_notes
Added: trunk/packages/primer3/trunk/debian/install
===================================================================
--- trunk/packages/primer3/trunk/debian/install 2006-08-23 14:43:00 UTC (rev 97)
+++ trunk/packages/primer3/trunk/debian/install 2006-08-23 14:53:19 UTC (rev 98)
@@ -0,0 +1,4 @@
+src/primer3_core usr/bin
+#src/primer*www*.html var/www
+#src/primer*www*.cgi usr/lib/cgi-bin
+
Added: trunk/packages/primer3/trunk/debian/manpages
===================================================================
--- trunk/packages/primer3/trunk/debian/manpages 2006-08-23 14:43:00 UTC (rev 97)
+++ trunk/packages/primer3/trunk/debian/manpages 2006-08-23 14:53:19 UTC (rev 98)
@@ -0,0 +1 @@
+primer3.1
Added: trunk/packages/primer3/trunk/debian/rules
===================================================================
--- trunk/packages/primer3/trunk/debian/rules 2006-08-23 14:43:00 UTC (rev 97)
+++ trunk/packages/primer3/trunk/debian/rules 2006-08-23 14:53:19 UTC (rev 98)
@@ -0,0 +1,68 @@
+#!/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
+
+build: build-stamp
+
+build-stamp:
+ dh_testdir
+
+ # Add here commands to compile the package.
+ $(MAKE) -C src
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp
+
+ # Add here commands to clean up after the build process.
+ -$(MAKE) -C src clean
+
+ dh_clean primer3_core.1 primer3.1
+
+primer3.1: primer3.sgml
+ docbook-to-man $< > $@
+
+install: build primer3.1
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installexamples example
+ dh_installman
+ dh_install
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-arch
+.PHONY: build clean binary-arch binary install configure
Property changes on: trunk/packages/primer3/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/primer3/trunk/primer3.sgml
===================================================================
--- trunk/packages/primer3/trunk/primer3.sgml 2006-08-23 14:43:00 UTC (rev 97)
+++ trunk/packages/primer3/trunk/primer3.sgml 2006-08-23 14:53:19 UTC (rev 98)
@@ -0,0 +1,115 @@
+<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
+
+ <!-- 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>March 31, 2004</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>PRIMER3</refentrytitle>">
+ <!ENTITY dhpackage "primer3">
+
+ <!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>Designs primers for PCR</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;_core</command>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+
+ <para>This manual page was written for the &debian; distribution
+ because the original program does not have a manual page.
+ </para>
+ <para>
+Primer3 determines oligos for the polymerase chain reaction (PCR) to create copies of a DNA sequence.
+Constrains on the oligos, like their minimal, desired and maximal length, melting temperature and many other criteria may be specified.
+ </para>
+ <para>
+The package installs a CGI script for the package in /usr/lib/cgi-bin with its help files in /var/www which works for single sequences. The package itself may be used for batch queries and is not interactive. It expects sequences to be piped in via stdin in a format descripted in detail in the README file. The web interface and its introduction is a good introduction, too.
+ </para>
+ <para>
+ The program was created by Steve Rozen and Helen J. Skaletsky (1996,1997,1998).
+ </para>
+
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+
+ <para>e-PCR (of the ncbi-epcr package) (1)</para>
+
+ <para>http://localhost/cgi-bin/primer3_www.cgi</para>
+
+ <para>The program is well described by the
+ <citetitle>README</citetitle> file available
+ in /usr/share/doc/primer3.
+ </para>
+ <para>http://www-genome.wi.mit.edu/genome_software/other/primer3.html</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:
+-->
+
+
Modified: trunk/packages/primer3/trunk/src/Makefile
===================================================================
--- trunk/packages/primer3/trunk/src/Makefile 2006-08-23 14:43:00 UTC (rev 97)
+++ trunk/packages/primer3/trunk/src/Makefile 2006-08-23 14:53:19 UTC (rev 98)
@@ -54,7 +54,9 @@
CFLAGS = $(CC_OPTS) $(O_OPTS)
LDFLAGS = -g
-LIBOPTS ='-static'
+LIBOPTS =
+#'-static'
+
PRIMER_EXE = primer3_core
PRIMER_OBJECTS=primer3_main.o\
@@ -71,6 +73,8 @@
clean:
-rm *.o $(EXES) *~
+distclean: clean
+
$(PRIMER_EXE): $(PRIMER_OBJECTS)
$(CC) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
Property changes on: trunk/packages/primer3/trunk/test/dpal_gen.pl
___________________________________________________________________
Name: svn:executable
-
+ *
Property changes on: trunk/packages/primer3/trunk/test/dpal_test.pl
___________________________________________________________________
Name: svn:executable
-
+ *
Property changes on: trunk/packages/primer3/trunk/test/long_seq_tm_test.pl
___________________________________________________________________
Name: svn:executable
-
+ *
Property changes on: trunk/packages/primer3/trunk/test/primer_test.pl
___________________________________________________________________
Name: svn:executable
-
+ *
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