[med-svn] r136 - trunk/packages/primer3/trunk/debian
Charles Plessy
charles-guest at costa.debian.org
Thu Sep 28 10:26:00 UTC 2006
Author: charles-guest
Date: 2006-09-28 10:25:57 +0000 (Thu, 28 Sep 2006)
New Revision: 136
Added:
trunk/packages/primer3/trunk/debian/oligotm.1.xml
Modified:
trunk/packages/primer3/trunk/debian/control
trunk/packages/primer3/trunk/debian/copyright
trunk/packages/primer3/trunk/debian/ntdpal.1.xml
trunk/packages/primer3/trunk/debian/primer3.dirs
trunk/packages/primer3/trunk/debian/primer3.docs
trunk/packages/primer3/trunk/debian/primer3.install
trunk/packages/primer3/trunk/debian/primer3.manpages
trunk/packages/primer3/trunk/debian/primer3_core.1.xml
trunk/packages/primer3/trunk/debian/rules
Log:
manpage for a new binary, and repairing things broken by the new upstream version. Enabling tests.
Modified: trunk/packages/primer3/trunk/debian/control
===================================================================
--- trunk/packages/primer3/trunk/debian/control 2006-09-28 06:23:57 UTC (rev 135)
+++ trunk/packages/primer3/trunk/debian/control 2006-09-28 10:25:57 UTC (rev 136)
@@ -9,7 +9,6 @@
Package: primer3
Architecture: any
Depends: ${shlibs:Depends}, ${misc: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
@@ -20,7 +19,8 @@
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.
+ 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.
Modified: trunk/packages/primer3/trunk/debian/copyright
===================================================================
--- trunk/packages/primer3/trunk/debian/copyright 2006-09-28 06:23:57 UTC (rev 135)
+++ trunk/packages/primer3/trunk/debian/copyright 2006-09-28 10:25:57 UTC (rev 136)
@@ -1,54 +1,38 @@
This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
-Wed, 31 Mar 2004 15:07:10 +0200.
+Wed, 31 Mar 2004 15:07:10 +0200. The packaging was finished in 2006 by Charles
+Plessy <charles-debian-nospam at plessy.org>. His packaging work is hereby
+released in the public domain unless stated otherwise.
-It was downloaded from: http://www-genome.wi.mit.edu/genome_software/other/primer3.html
+Primer3 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 (c) 1996,1997,1998,1999,2000,2001,2004,2006
+Whitehead Institute for Biomedical Research, Steve Rozen
+(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
+All rights reserved.
-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:
+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.
+ * Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form 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.
+ * Neither the names of the copyright holders nor contributors may
+be used to endorse or promote products derived from this software
+without specific prior written permission.
-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.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"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 COPYRIGHT
+OWNERS OR CONTRIBUTORS 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.
-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.
Modified: trunk/packages/primer3/trunk/debian/ntdpal.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/ntdpal.1.xml 2006-09-28 06:23:57 UTC (rev 135)
+++ trunk/packages/primer3/trunk/debian/ntdpal.1.xml 2006-09-28 10:25:57 UTC (rev 136)
@@ -200,7 +200,7 @@
<refsect1>
<title>SEE ALSO</title>
- <para>primer3_core (1)</para>
+ <para>primer3_core (1), oligotm (1)</para>
</refsect1>
<refsect1>
Added: trunk/packages/primer3/trunk/debian/oligotm.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/oligotm.1.xml (rev 0)
+++ trunk/packages/primer3/trunk/debian/oligotm.1.xml 2006-09-28 10:25:57 UTC (rev 136)
@@ -0,0 +1,135 @@
+<?xml version='1.0' encoding='ISO-8859-1'?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
+ <!ENTITY dhfirstname "<firstname>CHARLES</firstname>">
+ <!ENTITY dhsurname "<surname>PLESSY</surname>">
+ <!ENTITY dhdate "<date>September 28, 2006</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
+ <!ENTITY dhusername "Charles Plessy">
+ <!ENTITY dhucpackage "<refentrytitle>OLIGOTM</refentrytitle>">
+ <!ENTITY dhpackage "oligotm">
+ <!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>2006</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>Prints oligo's melting temperature on stdout.</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt">-k <replaceable class="parameter">salt-conc</replaceable></arg>
+ <arg choice="opt">-d <replaceable class="parameter">template-conc</replaceable></arg>
+ <arg choice="req"><replaceable class="parameter">oligo</replaceable></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+
+ <para>
+ <command>&dhpackage;</command> prints the melting temperature of a given desoxyribooligonucleotide on the standard output. It is part of the Primer3 package.
+ </para>
+ </refsect1>
+
+ <refsect1>
+ <title>OPTIONS</title>
+
+ <variablelist>
+ <varlistentry>
+ <term>
+ <option>-k</option> <parameter>salt-conc</parameter>
+ </term>
+ <listitem>
+ <para><parameter>salt-conc</parameter> is mM salt (usually K) concentration; defaults to 50mM.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-t</option> <parameter>template-conc</parameter>
+ </term>
+ <listitem>
+ <para><parameter>template-conc</parameter> is nM template concentration; defaults to 50nM.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <refsect1>
+ <title>REFERENCE</title>
+ <para>
+ Please cite 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.
+ </para>
+ </refsect1>
+
+ <refsect1>
+ <title>SEE ALSO</title>
+
+ <para>primer3_core (1), ntdpal (1).</para>
+
+ </refsect1>
+ <refsect1>
+ <title>COPYRIGHTS</title>
+
+ <para>
+ Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006 Steve Rozen, Helen Skaletsky, and Whitehead
+ Institute for Biomedical Research. On Debian-based systems, please consult
+ <filename>/usr/share/doc/primer3/copyright</filename> to read the licence
+ of &dhpackage;.
+ </para>
+
+ <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 same terms as Primer3 itself.<!-- This also applies to this source document -->
+ </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/debian/primer3.dirs
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3.dirs 2006-09-28 06:23:57 UTC (rev 135)
+++ trunk/packages/primer3/trunk/debian/primer3.dirs 2006-09-28 10:25:57 UTC (rev 136)
@@ -1,3 +1,2 @@
usr/bin
-usr/lib/cgi-bin
-var/www
+usr/share/doc/primer3
Modified: trunk/packages/primer3/trunk/debian/primer3.docs
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3.docs 2006-09-28 06:23:57 UTC (rev 135)
+++ trunk/packages/primer3/trunk/debian/primer3.docs 2006-09-28 10:25:57 UTC (rev 136)
@@ -1,2 +1,3 @@
-README
-src/release_notes
+README.primer3_1.0b.txt
+src/release_notes.txt
+how-to-cite.txt
Modified: trunk/packages/primer3/trunk/debian/primer3.install
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3.install 2006-09-28 06:23:57 UTC (rev 135)
+++ trunk/packages/primer3/trunk/debian/primer3.install 2006-09-28 10:25:57 UTC (rev 136)
@@ -1,5 +1,4 @@
src/primer3_core usr/bin
src/ntdpal usr/bin
-#src/primer*www*.html var/www
-#src/primer*www*.cgi usr/lib/cgi-bin
-
+src/oligotm usr/bin
+#src/long_seq_tm_test usr/bin
Modified: trunk/packages/primer3/trunk/debian/primer3.manpages
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3.manpages 2006-09-28 06:23:57 UTC (rev 135)
+++ trunk/packages/primer3/trunk/debian/primer3.manpages 2006-09-28 10:25:57 UTC (rev 136)
@@ -1,2 +1,3 @@
debian/ntdpal.1
debian/primer3_core.1
+debian/oligotm.1
Modified: trunk/packages/primer3/trunk/debian/primer3_core.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3_core.1.xml 2006-09-28 06:23:57 UTC (rev 135)
+++ trunk/packages/primer3/trunk/debian/primer3_core.1.xml 2006-09-28 10:25:57 UTC (rev 136)
@@ -115,7 +115,7 @@
<refsect1>
<title>SEE ALSO</title>
- <para>ntdpal (1)</para>
+ <para>ntdpal (1), oligotm (1).</para>
</refsect1>
<refsect1>
Modified: trunk/packages/primer3/trunk/debian/rules
===================================================================
--- trunk/packages/primer3/trunk/debian/rules 2006-09-28 06:23:57 UTC (rev 135)
+++ trunk/packages/primer3/trunk/debian/rules 2006-09-28 10:25:57 UTC (rev 136)
@@ -21,20 +21,25 @@
SKIP_TEST_CPUS := arm m68k s390
+PRIMER_EXE = primer3_core
+EXES=$(PRIMER_EXE) ntdpal oligotm long_seq_tm_test
+
build: manpages
dh_testdir
- $(MAKE) -C src all ntdpal
+ $(MAKE) -C src all LIBOPTS=''
touch build-stamp
build-stamp: build
+tests-stamp: tests
+
tests: build-stamp tests-clean
ifeq (,$(filter $(DEB_HOST_ARCH_CPU),$(SKIP_TEST_CPUS)))
cp -al test tests
- cd tests ; cow-shell perl primer_test.pl ; cow-shell perl long_seq_tm_test.pl ; cow-shell perl dpal_gen.pl; cow-shell perl dpal_test.pl
+ cd tests ; cow-shell perl p3test.pl ; cow-shell perl dpal_test.pl
else
- @echo "Slow-cpu arch detected, skipping test"
+ @echo "Slow-cpu arch detected, skipping test"
endif
touch tests-stamp
@@ -46,10 +51,10 @@
dh_testroot
rm -f build-stamp
- # Add here commands to clean up after the build process.
- -$(MAKE) -C src clean
+ # make clean fails on clean sources, so I clean with this:
+ cd src ; rm -f *.o $(EXES) *~
- dh_clean debian/primer3_core.1 debian/ntdpal.1 debian/manpages
+ dh_clean debian/primer3_core.1 debian/ntdpal.1 debian/oligotm.1 debian/manpages
debian/primer3_core.1: debian/primer3_core.1.xml
xsltproc -o debian/ -''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl $<
@@ -57,7 +62,10 @@
debian/ntdpal.1: debian/ntdpal.1.xml
xsltproc -o debian/ -''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl $<
-manpages: debian/primer3_core.1 debian/ntdpal.1
+debian/oligotm.1: debian/oligotm.1.xml
+ xsltproc -o debian/ -''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl $<
+
+manpages: debian/primer3_core.1 debian/ntdpal.1 debian/oligotm.1
touch debian/manpages
install: build
@@ -67,7 +75,7 @@
dh_installdirs
# Build architecture-dependent files here.
-binary-arch: build install
+binary-arch: build install tests-stamp
dh_testdir
dh_testroot
dh_installchangelogs
@@ -85,5 +93,7 @@
dh_md5sums
dh_builddeb
+binary-indep:
+
binary: binary-arch
.PHONY: build clean binary-arch binary install configure
More information about the debian-med-commit
mailing list