[med-svn] r108 - trunk/packages/primer3/trunk/debian
Charles Plessy
charles-guest at costa.debian.org
Wed Sep 13 15:38:21 UTC 2006
Author: charles-guest
Date: 2006-09-13 15:38:20 +0000 (Wed, 13 Sep 2006)
New Revision: 108
Added:
trunk/packages/primer3/trunk/debian/primer3_core.1.xml
Removed:
trunk/packages/primer3/trunk/debian/README.Debian
Modified:
trunk/packages/primer3/trunk/debian/control
trunk/packages/primer3/trunk/debian/ntdpal.1.xml
trunk/packages/primer3/trunk/debian/primer3.manpages
trunk/packages/primer3/trunk/debian/rules
Log:
updating and enhancing manpages
Deleted: trunk/packages/primer3/trunk/debian/README.Debian
===================================================================
--- trunk/packages/primer3/trunk/debian/README.Debian 2006-09-08 04:21:26 UTC (rev 107)
+++ trunk/packages/primer3/trunk/debian/README.Debian 2006-09-13 15:38:20 UTC (rev 108)
@@ -1,15 +0,0 @@
-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
Modified: trunk/packages/primer3/trunk/debian/control
===================================================================
--- trunk/packages/primer3/trunk/debian/control 2006-09-08 04:21:26 UTC (rev 107)
+++ trunk/packages/primer3/trunk/debian/control 2006-09-13 15:38:20 UTC (rev 108)
@@ -3,12 +3,12 @@
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
+Build-Depends: debhelper (>= 5), docbook-to-man, xsltproc, docbook-xsl, docbook-xml, cowdancer
Standards-Version: 3.7.2
Package: primer3
Architecture: any
-Depends:
+Depends: ${shlibs:Depends}, ${misc:Depends}
Recommends: libcgi-perl, apache | httpd
Suggests: ncbi-epcr
Description: [Biology] Tool to design flanking oligo nucleotides for DNA amplification
Modified: trunk/packages/primer3/trunk/debian/ntdpal.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/ntdpal.1.xml 2006-09-08 04:21:26 UTC (rev 107)
+++ trunk/packages/primer3/trunk/debian/ntdpal.1.xml 2006-09-13 15:38:20 UTC (rev 108)
@@ -207,7 +207,7 @@
<title>COPYRIGHTS</title>
<para>
- Copyright (c) 1996, 2002, Steve Rozen, Helen Skaletsky, and Whitehead
+ 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;.
@@ -216,7 +216,7 @@
<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 &dhpackage; itself.
+ the same terms as Primer3 itself.
</para>
</refsect1>
Modified: trunk/packages/primer3/trunk/debian/primer3.manpages
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3.manpages 2006-09-08 04:21:26 UTC (rev 107)
+++ trunk/packages/primer3/trunk/debian/primer3.manpages 2006-09-13 15:38:20 UTC (rev 108)
@@ -1,2 +1,2 @@
-debian/ntdpal
-debian/primer3.1
+debian/ntdpal.1
+debian/primer3_core.1
Added: trunk/packages/primer3/trunk/debian/primer3_core.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3_core.1.xml (rev 0)
+++ trunk/packages/primer3/trunk/debian/primer3_core.1.xml 2006-09-13 15:38:20 UTC (rev 108)
@@ -0,0 +1,132 @@
+<?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>Steffen</firstname>">
+ <!ENTITY dhsurname "<surname>Moeller</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>September 13, 2006</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>steffen_moeller at gmx.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>PRIMER3_CORE</refentrytitle>">
+ <!ENTITY dhpackage "primer3_core">
+ <!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, 2006</year>
+ <holder>&dhusername;, Charles Plessy</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>Designs primers for PCR</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt">-format_output</arg>
+ <arg choice="opt">-2x_compat</arg>
+ <arg choice="opt">-strict_tags</arg>
+ <arg choice="opt">< <replaceable>input_file</replaceable></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+
+ <refsect1>
+ <title>DESCRIPTION</title>
+
+ <para>
+ &dhpackage; 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.
+ </para>
+ <para>
+ By default, &dhpackage; accepts input and produces output in Boulder-io format, a pre-XML text-based input/output format for program-to-program data interchange format. The Boulder-io format and the commands that &dhpackage; understands are described in the <filename>README</filename> file, which on Debian systems can be found in <filename class="directory">/usr/share/doc/primer3/</filename>.
+ </para>
+ </refsect1>
+
+ <refsect1>
+ <title>OPTIONS</title>
+
+ <variablelist>
+ <varlistentry>
+ <term>
+ <option>-format_output</option>
+ </term>
+ <listitem>
+ <para> Prints a more user-oriented report for each sequence.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-2x_compat</option>
+ </term>
+ <listitem>
+ <para>Print the output using Primer v2 compatible tag names.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-strict_tags</option>
+ </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.
+ </para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <refsect1>
+ <title>EXIT STATUS CODES</title>
+ <itemizedlist>
+ <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>
+ <listitem><para>-4 error in a "Global" input tag (message in PRIMER_ERROR).</para></listitem>
+ </itemizedlist>
+ </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>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; and Charles Plessy 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.
+ </para>
+ </refsect1>
+</refentry>
+
Modified: trunk/packages/primer3/trunk/debian/rules
===================================================================
--- trunk/packages/primer3/trunk/debian/rules 2006-09-08 04:21:26 UTC (rev 107)
+++ trunk/packages/primer3/trunk/debian/rules 2006-09-13 15:38:20 UTC (rev 108)
@@ -17,35 +17,55 @@
INSTALL_PROGRAM += -s
endif
-build: build-stamp
+DEB_HOST_ARCH_CPU ?= $(shell dpkg-architecture -qDEB_HOST_ARCH_CPU)
-build-stamp:
+SKIP_TEST_CPUS := arm m68k s390
+
+
+build: manpages
dh_testdir
-
- # Add here commands to compile the package.
$(MAKE) -C src all ntdpal
touch build-stamp
-clean:
+build-stamp: build
+
+tests: build-stamp tests-clean
+ifeq (,$(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 ..
+else
+ @echo "Slow-cpu arch detected, skipping test"
+endif
+ touch tests-stamp
+
+tests-clean:
+ rm -rf tests tests-stamp
+
+clean: tests-clean
dh_testdir
dh_testroot
- rm -f build-stamp configure-stamp
+ rm -f build-stamp
# Add here commands to clean up after the build process.
-$(MAKE) -C src clean
- dh_clean debian/primer3.1 debian/ntdpal.1 debian/manpages
+ dh_clean debian/primer3_core.1 debian/ntdpal.1 debian/manpages
-debian/primer3.1: debian/primer3.sgml
- docbook-to-man $< > $@
+debian/primer3_core.1: debian/primer3_core.1.xml
+ xsltproc -o debian/ -''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl $<
debian/ntdpal.1: debian/ntdpal.1.xml
xsltproc -o debian/ -''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl $<
-manpages: debian/primer3.1 debian/ntdpal.1
+manpages: debian/primer3_core.1 debian/ntdpal.1
touch debian/manpages
-install: build manpages
+install: build
dh_testdir
dh_testroot
dh_clean -k
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