[med-svn] r109 - trunk/packages/primer3/trunk/debian
Charles Plessy
charles-guest at costa.debian.org
Thu Sep 14 02:32:00 UTC 2006
Author: charles-guest
Date: 2006-09-14 02:32:00 +0000 (Thu, 14 Sep 2006)
New Revision: 109
Removed:
trunk/packages/primer3/trunk/debian/primer3.sgml
Modified:
trunk/packages/primer3/trunk/debian/changelog
trunk/packages/primer3/trunk/debian/primer3_core.1.xml
trunk/packages/primer3/trunk/debian/rules
Log:
Modification of manpage, fix test rule in debian/rules
Modified: trunk/packages/primer3/trunk/debian/changelog
===================================================================
--- trunk/packages/primer3/trunk/debian/changelog 2006-09-13 15:38:20 UTC (rev 108)
+++ trunk/packages/primer3/trunk/debian/changelog 2006-09-14 02:32:00 UTC (rev 109)
@@ -4,9 +4,10 @@
* 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.
+ * Using debhelper v5.
+ * Relicencing the manpage of Primer3 (thanks to Steffen Moeller).
- -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 23 Aug 2006 22:06:24 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Thu, 14 Sep 2006 11:30:04 +0900
primer3 (0.9-0.2) unstable; urgency=low
Deleted: trunk/packages/primer3/trunk/debian/primer3.sgml
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3.sgml 2006-09-13 15:38:20 UTC (rev 108)
+++ trunk/packages/primer3/trunk/debian/primer3.sgml 2006-09-14 02:32:00 UTC (rev 109)
@@ -1,115 +0,0 @@
-<!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/debian/primer3_core.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3_core.1.xml 2006-09-13 15:38:20 UTC (rev 108)
+++ trunk/packages/primer3/trunk/debian/primer3_core.1.xml 2006-09-14 02:32:00 UTC (rev 109)
@@ -88,7 +88,7 @@
</term>
<listitem>
<para>
- &dhpackage; echos and ignores any tags it does not recognize, unless the <option>-strict_tags</option> flag is set on the command line, in which case &dhpackage; prints an error in the PRIMER_ERROR output tag, and prints additional information on stdout; this option can be useful for debugging systems that incorporate primer.
+ &dhpackage; echoes and ignores any tags it does not recognize, unless the <option>-strict_tags</option> flag is set on the command line, in which case &dhpackage; prints an error in the PRIMER_ERROR output tag, and prints additional information on stdout; this option can be useful for debugging systems that incorporate primer.
</para>
</listitem>
</varlistentry>
@@ -98,7 +98,7 @@
<refsect1>
<title>EXIT STATUS CODES</title>
<itemizedlist>
- <listitem><para>0 on normal operation.</para></listitem>
+ <listitem><para> 0 on normal operation.</para></listitem>
<listitem><para>-1 under the following conditions: illegal command-line arguments, unable to fflush stdout, unable to open (for writing and creating) a .for, .rev or .int file (probably due to a protection problem).</para></listitem>
<listitem><para>-2 on out-of-memory.</para></listitem>
<listitem><para>-3 empty input.</para></listitem>
Modified: trunk/packages/primer3/trunk/debian/rules
===================================================================
--- trunk/packages/primer3/trunk/debian/rules 2006-09-13 15:38:20 UTC (rev 108)
+++ trunk/packages/primer3/trunk/debian/rules 2006-09-14 02:32:00 UTC (rev 109)
@@ -32,12 +32,7 @@
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 ..
+ 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
else
@echo "Slow-cpu arch detected, skipping test"
endif
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