[med-svn] r90 - in trunk/packages/perlprimer/trunk: . debian
Charles Plessy
charles-guest at costa.debian.org
Mon Aug 7 14:01:20 UTC 2006
Author: charles-guest
Date: 2006-08-07 14:01:18 +0000 (Mon, 07 Aug 2006)
New Revision: 90
Added:
trunk/packages/perlprimer/trunk/debian/
trunk/packages/perlprimer/trunk/debian/README.Debian
trunk/packages/perlprimer/trunk/debian/changelog
trunk/packages/perlprimer/trunk/debian/compat
trunk/packages/perlprimer/trunk/debian/control
trunk/packages/perlprimer/trunk/debian/copyright
trunk/packages/perlprimer/trunk/debian/perlprimer-doc.dirs
trunk/packages/perlprimer/trunk/debian/perlprimer-doc.doc-base
trunk/packages/perlprimer/trunk/debian/perlprimer.desktop
trunk/packages/perlprimer/trunk/debian/perlprimer.dirs
trunk/packages/perlprimer/trunk/debian/perlprimer.docs
trunk/packages/perlprimer/trunk/debian/perlprimer.manpages
trunk/packages/perlprimer/trunk/debian/perlprimer.menu
trunk/packages/perlprimer/trunk/debian/rules
trunk/packages/perlprimer/trunk/debian/watch
trunk/packages/perlprimer/trunk/perlprimer.1
Modified:
trunk/packages/perlprimer/trunk/perlprimer.pl
Log:
Load perlprimer-1.1.13 into trunk/packages/./perlprimer/trunk.
Added: trunk/packages/perlprimer/trunk/debian/README.Debian
===================================================================
--- trunk/packages/perlprimer/trunk/debian/README.Debian 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/debian/README.Debian 2006-08-07 14:01:18 UTC (rev 90)
@@ -0,0 +1,9 @@
+perlprimer for Debian
+---------------------
+
+The REBASE file is ok to be included with PerlPrimer, this was
+checked with the REBASE maintainer.
+
+Steffen
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>, Thu, 6 Jan 2005 22:00:24 +0100
Added: trunk/packages/perlprimer/trunk/debian/changelog
===================================================================
--- trunk/packages/perlprimer/trunk/debian/changelog 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/debian/changelog 2006-08-07 14:01:18 UTC (rev 90)
@@ -0,0 +1,20 @@
+perlprimer (1.1.13-1) unstable; urgency=low
+
+ [ Steffen Moeller ]
+ * New maintainer email address.
+ * REBASE database was updated.
+ * Updated doc-base entry.
+
+ [ Charles Plessy ]
+ * New upstream release (Closes: #364237).
+ * Added desktop file.
+ * Added menu icon.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Fri, 4 Aug 2006 23:40:49 +0900
+
+perlprimer (1.1.8-1) unstable; urgency=low
+
+ * Initial Release (Closes: #289043).
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Thu, 6 Jan 2005 22:00:24 +0100
+
Added: trunk/packages/perlprimer/trunk/debian/compat
===================================================================
--- trunk/packages/perlprimer/trunk/debian/compat 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/debian/compat 2006-08-07 14:01:18 UTC (rev 90)
@@ -0,0 +1 @@
+4
Added: trunk/packages/perlprimer/trunk/debian/control
===================================================================
--- trunk/packages/perlprimer/trunk/debian/control 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/debian/control 2006-08-07 14:01:18 UTC (rev 90)
@@ -0,0 +1,33 @@
+Source: perlprimer
+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 (>= 4.0.0)
+Standards-Version: 3.7.2
+
+Package: perlprimer
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, perl-tk, libwww-perl
+Recommends: ncbi-tools-bin
+Suggests: perlprimer-doc
+Description: [Biology] graphical design of primers for PCR
+ PerlPrimer is a free, open-source GUI application written in Perl
+ that designs primers for standard PCR, bisulphite PCR, real-time PCR
+ (QPCR) and sequencing. It aims to automate and simplify the process of
+ primer design.
+ .
+ It nicely communicates with the Ensembl project if online for further
+ insights into the gene structure.
+ .
+ Homepage: http://perlprimer.sourceforge.net
+
+Package: perlprimer-doc
+Architecture: all
+Section: doc
+Suggests: perlprimer
+Description: [Biology] tutorial to perlprimer
+ An HTML tutorial explaining the use of the user interface and
+ utilisation of online resources.
+ .
+ Homepage: http://perlprimer.sourceforge.net
Added: trunk/packages/perlprimer/trunk/debian/copyright
===================================================================
--- trunk/packages/perlprimer/trunk/debian/copyright 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/debian/copyright 2006-08-07 14:01:18 UTC (rev 90)
@@ -0,0 +1,26 @@
+This package was debianized by Steffen Moeller <steffen_moeller at gmx.de> on
+Thu, 6 Jan 2005 22:00:24 +0100.
+
+It was downloaded from http://perlprimer.sourceforge.net
+
+Copyright Holder: Owen Marshall <owenjm at users.sourceforge.net>
+
+License:
+
+ This package is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
+
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+On Debian systems, the complete text of the GNU Lesser General
+Public License can be found in `/usr/share/common-licenses/LGPL'.
+
Added: trunk/packages/perlprimer/trunk/debian/perlprimer-doc.dirs
===================================================================
--- trunk/packages/perlprimer/trunk/debian/perlprimer-doc.dirs 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/debian/perlprimer-doc.dirs 2006-08-07 14:01:18 UTC (rev 90)
@@ -0,0 +1 @@
+usr/share/doc/perlprimer
Added: trunk/packages/perlprimer/trunk/debian/perlprimer-doc.doc-base
===================================================================
--- trunk/packages/perlprimer/trunk/debian/perlprimer-doc.doc-base 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/debian/perlprimer-doc.doc-base 2006-08-07 14:01:18 UTC (rev 90)
@@ -0,0 +1,13 @@
+Document: perlprimer
+Title: Debian perlprimer Tutorial
+Author: Owen Marshall <owenjm at users.sourceforge.net>
+Abstract: This tutorial introduces to the
+ PerlPrimer user interface and the utilisation
+ of online resources.
+Section: Apps/Science
+
+Format: HTML
+Index: /usr/share/doc/perlprimer/tutorial.html
+Files: /usr/share/doc/perlprimer/tutorial.html /usr/share/doc/perlprimer/tutorial_files/*
+
+
Added: trunk/packages/perlprimer/trunk/debian/perlprimer.desktop
===================================================================
--- trunk/packages/perlprimer/trunk/debian/perlprimer.desktop 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/debian/perlprimer.desktop 2006-08-07 14:01:18 UTC (rev 90)
@@ -0,0 +1,18 @@
+[Desktop Entry]
+Version=1.0
+Encoding=UTF-8
+Terminal=false
+Icon=perlprimer
+Exec=perlprimer %U
+Name=PerlPrimer
+GenericName=Primer design
+GenericName[en]=Primer design
+GenericName[fr]=Conception d'amorces
+GenericName[pt_BR]=Projeto de primer
+Comment=Graphical design of primers for PCR and sequencing
+Comment[en]=Graphical design of primers for PCR and sequencing
+Comment[fr]=Conception d'amorces de PCR et de séquençage
+Comment[pt_BR]=Projeto gráfico de primers para PCR e sequenciamento
+Type=Application
+Categories=Biology;Science;Education;
+
Added: trunk/packages/perlprimer/trunk/debian/perlprimer.dirs
===================================================================
--- trunk/packages/perlprimer/trunk/debian/perlprimer.dirs 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/debian/perlprimer.dirs 2006-08-07 14:01:18 UTC (rev 90)
@@ -0,0 +1,5 @@
+usr/bin
+usr/share/perlprimer
+/usr/share/pixmaps/
+/usr/share/applications/
+
Added: trunk/packages/perlprimer/trunk/debian/perlprimer.docs
===================================================================
--- trunk/packages/perlprimer/trunk/debian/perlprimer.docs 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/debian/perlprimer.docs 2006-08-07 14:01:18 UTC (rev 90)
@@ -0,0 +1,2 @@
+todo
+ReadMe.txt
Added: trunk/packages/perlprimer/trunk/debian/perlprimer.manpages
===================================================================
--- trunk/packages/perlprimer/trunk/debian/perlprimer.manpages 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/debian/perlprimer.manpages 2006-08-07 14:01:18 UTC (rev 90)
@@ -0,0 +1 @@
+perlprimer.1
Added: trunk/packages/perlprimer/trunk/debian/perlprimer.menu
===================================================================
--- trunk/packages/perlprimer/trunk/debian/perlprimer.menu 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/debian/perlprimer.menu 2006-08-07 14:01:18 UTC (rev 90)
@@ -0,0 +1,8 @@
+?package(perlprimer):\
+ needs="X11"\
+ section="Apps/Science"\
+ title="PerlPrimer"\
+ command="/usr/bin/perlprimer"\
+ icon="/usr/share/pixmaps/perlprimer.xpm"\
+ hints="Primer design"\
+ longtitle="PerlPrimer: graphical design of primers for PCR and sequencing"
Added: trunk/packages/perlprimer/trunk/debian/rules
===================================================================
--- trunk/packages/perlprimer/trunk/debian/rules 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/debian/rules 2006-08-07 14:01:18 UTC (rev 90)
@@ -0,0 +1,69 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# 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
+
+clean:
+ dh_testdir
+ dh_testroot
+
+ dh_clean
+
+install:
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+ # Add here commands to install the package into debian/perlprimer.
+ cp perlprimer.pl $(CURDIR)/debian/perlprimer/usr/bin/perlprimer
+ cp gcg.603 $(CURDIR)/debian/perlprimer/usr/share/perlprimer
+ cp -r tutorial.html tutorial_files $(CURDIR)/debian/perlprimer-doc/usr/share/doc/perlprimer/
+ perl -ne '$$found= 0 if /end_of_pixmap/ ; print if $$found ;$$found = 1 if /perlprimer_icon =/' < perlprimer.pl > $(CURDIR)/debian/perlprimer/usr/share/pixmaps/perlprimer.xpm
+ install -m 644 debian/perlprimer.desktop $(CURDIR)/debian/perlprimer/usr/share/applications
+
+# Build architecture-dependent files here.
+binary-arch: build install
+# We have nothing to do
+
+build:
+# We have nothing to do
+
+
+# Build architecture-independent files here.
+binary-indep: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs Changelog
+ dh_installdocs
+ dh_installmenu
+ dh_desktop
+ dh_installman
+ dh_compress
+ dh_fixperms
+ dh_perl
+ 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/perlprimer/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/perlprimer/trunk/debian/watch
===================================================================
--- trunk/packages/perlprimer/trunk/debian/watch 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/debian/watch 2006-08-07 14:01:18 UTC (rev 90)
@@ -0,0 +1,8 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# Site Directory Pattern Version Script
+version=3
+# Uncomment to use Roland's hack for sourceforge based projects - YMMV!
+http://people.debian.org/~lolando/sfdlr.php?project=perlprimer perlprimer-([\d.]*).tar.bz2
+
Added: trunk/packages/perlprimer/trunk/perlprimer.1
===================================================================
--- trunk/packages/perlprimer/trunk/perlprimer.1 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/perlprimer.1 2006-08-07 14:01:18 UTC (rev 90)
@@ -0,0 +1,21 @@
+.\" Hey, EMACS: -*- nroff -*-
+.TH PERLPRIMER 1 "6 January 2005"
+.SH NAME
+perlprimer \- graphically specify amplicon of DNA or mRNA sequences and design primers
+.SH SYNOPSIS
+.B perlprimer
+.SH DESCRIPTION
+.B PerlPrimer
+calculates primer melting temperature using J. SantaLucia's extensive nearest-neighbour thermodynamic parameters. To adjust for the salt conditions of the PCR, PerlPrimer uses the empirical formula derived by von Ahsen, et al. (2001) and allows the user to specify the concentration of Mg2+, dNTPs and primers, or use standard PCR conditions. The result is a highly accurate prediction of primer melting temperature, giving rise to a maximum yeild of product when amplified.
+.BR
+PerlPrimer is written in Perl and requires Perl/Tk. In addition, for QPCR functionality PerlPrimer requires the open-source Spidey executable from NCBI. The program is designed to be cross-platform compatible and has been developed and tested on both Microsoft Windows and GNU/Linux-based operating systems. Users have also reported success using the program under Mac OS X.
+.SH SEE ALSO
+.BR
+A very nice tutorial on http://perlprimer.sourceforge.net is also distributed
+as a debian package perlprimer-doc.
+.br
+.SH AUTHOR
+perlprimer was written by Owen Marshall <owenjm at users.sourceforge.net>
+.PP
+This manual page was assembled by Steffen Moeller <steffen_moeller at gmx.de>,
+for the Debian project (but may be used by others).
Modified: trunk/packages/perlprimer/trunk/perlprimer.pl
===================================================================
--- trunk/packages/perlprimer/trunk/perlprimer.pl 2006-08-07 13:34:09 UTC (rev 89)
+++ trunk/packages/perlprimer/trunk/perlprimer.pl 2006-08-07 14:01:18 UTC (rev 90)
@@ -18,7 +18,7 @@
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
# USA
use strict;
@@ -3832,7 +3832,15 @@
# search for the file in the program directory
@gcg_paths = glob("$program_directory"."gcg.*");
}
-
+ unless (@gcg_paths) {
+ # search for the file where it should be
+ @gcg_paths = glob("/usr/share/perlprimer/"."gcg.*");
+ }
+ unless (@gcg_paths) {
+ # search for the file in the current directory
+ @gcg_paths = glob("./"."gcg.*");
+ }
+
my $gcg_path;
foreach (@gcg_paths) {
if (/.*gcg\.\d*$/) {
Property changes on: trunk/packages/perlprimer/trunk/perlprimer.pl
___________________________________________________________________
Name: svn:executable
-
+ *
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