[med-svn] r7792 - in trunk/packages: . plato plato/trunk plato/trunk/debian plato/trunk/debian/source

Wed Sep 14 14:10:31 UTC 2011

Author: moeller
Date: 2011-09-14 14:10:31 +0000 (Wed, 14 Sep 2011)
New Revision: 7792

Added:
   trunk/packages/plato/
   trunk/packages/plato/trunk/
   trunk/packages/plato/trunk/debian/
   trunk/packages/plato/trunk/debian/README.Debian
   trunk/packages/plato/trunk/debian/README.source
   trunk/packages/plato/trunk/debian/changelog
   trunk/packages/plato/trunk/debian/compat
   trunk/packages/plato/trunk/debian/control
   trunk/packages/plato/trunk/debian/copyright
   trunk/packages/plato/trunk/debian/docs
   trunk/packages/plato/trunk/debian/plato.install
   trunk/packages/plato/trunk/debian/rules
   trunk/packages/plato/trunk/debian/source/
   trunk/packages/plato/trunk/debian/source/format
   trunk/packages/plato/trunk/debian/watch
Log:
Just to help my local needs/education a bit, I just completed
the compilation of plato. Again, copyright information is still
missing. Once more I hope for a volunteer to complete the 
packaging.

Steffen

W: plato: new-package-should-close-itp-bug
W: plato: wrong-bug-number-in-closes l3:#nnnn
E: plato: helper-templates-in-copyright
E: plato: helper-templates-in-copyright
E: plato: helper-templates-in-copyright
W: plato: copyright-has-url-from-dh_make-boilerplate
E: plato: copyright-contains-dh_make-todo-boilerplate
W: plato: readme-debian-contains-debmake-template
W: plato: binary-without-manpage usr/bin/plato



Added: trunk/packages/plato/trunk/debian/README.Debian
===================================================================

--- trunk/packages/plato/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/plato/trunk/debian/README.Debian	2011-09-14 14:10:31 UTC (rev 7792)
@@ -0,0 +1,6 @@
+plato for Debian
+----------------
+
+<possible notes regarding this package - if none, delete this file>
+
+ -- Steffen Moeller <moeller at debian.org>  Wed, 14 Sep 2011 14:47:35 +0200

Added: trunk/packages/plato/trunk/debian/README.source
===================================================================
--- trunk/packages/plato/trunk/debian/README.source	                        (rev 0)
+++ trunk/packages/plato/trunk/debian/README.source	2011-09-14 14:10:31 UTC (rev 7792)
@@ -0,0 +1,9 @@
+plato for Debian
+----------------
+
+<this file describes information about the source package, see Debian policy
+manual section 4.14. You WILL either need to modify or delete this file>
+
+
+
+

Added: trunk/packages/plato/trunk/debian/changelog
===================================================================
--- trunk/packages/plato/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/plato/trunk/debian/changelog	2011-09-14 14:10:31 UTC (rev 7792)
@@ -0,0 +1,5 @@
+plato (1.1-1) unstable; urgency=low
+
+  * Initial release (Closes: #nnnn)  <nnnn is the bug number of your ITP>
+
+ -- Steffen Moeller <moeller at debian.org>  Wed, 14 Sep 2011 14:47:35 +0200

Added: trunk/packages/plato/trunk/debian/compat
===================================================================
--- trunk/packages/plato/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/plato/trunk/debian/compat	2011-09-14 14:10:31 UTC (rev 7792)
@@ -0,0 +1 @@
+8

Added: trunk/packages/plato/trunk/debian/control
===================================================================
--- trunk/packages/plato/trunk/debian/control	                        (rev 0)
+++ trunk/packages/plato/trunk/debian/control	2011-09-14 14:10:31 UTC (rev 7792)
@@ -0,0 +1,65 @@
+Source: plato
+Section: science
+Priority: extra
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 8.0.0),
+ libboost-dev
+Standards-Version: 3.9.2
+Homepage: https://chgr.mc.vanderbilt.edu/plato
+#Vcs-Git: git://git.debian.org/collab-maint/plato.git
+#Vcs-Browser: http://git.debian.org/?p=collab-maint/plato.git;a=summary
+
+Package: plato
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Analysis, translation, and organization of large-scale genetic data
+ PLATO is an acronym for "PLatform for the Analysis, Translation,
+ and Organization of large-scale data".  Recent technological advances
+ enable the study of hundreds of thousands of human single-nucleotide
+ polymorphisms at the population level. Because strategies for analyzing
+ these data have not kept pace with the laboratory methods that generate
+ the data, it is unlikely that these advances will immediately lead to
+ an improved understanding of the genetic contribution to common human
+ disease and drug response. Currently, no single analytical method
+ allows us to extract all available information from a whole-genome
+ association study. In fact, no single method can be optimal for all
+ datasets, especially when the genetic architecture for diseases can
+ vary substantially, as is certainly the case. Therefore, an integrative
+ platform is needed to accommodate multiple analytical methods for
+ analysis as we learn more about genetic architecture. As a result,
+ we are developing a system for the analysis of genome-wide association
+ data that will incorporate several analytical approaches as filters to
+ allow a scientist to choose whatever analytical methods they wish to
+ apply. PLATO (PLatform for the Analysis, Translation, and Organization
+ of large-scale data) will incorporate a number of filters to select
+ the important SNPs in a genome-wide association study.
+ .
+ Whole-genome Association Study Pipeline (WASP) has recently been
+ absorbed into PLATO. WASP was designed to aid in retrieving, evaluating,
+ formatting, and analyzing genotypic and clinical data from the latest
+ large-scale genotyping studies. WASP implements a battery of quality
+ control procedures to assess the data. Among the currently available
+ procedures are the examination of marker and sample genotyping
+ efficiency, allele frequency calculations, checks of Mendelian error
+ (if applicable) and gender discrepancies (based on available chromosome X
+ and Y genotypes), and tests of Hardy-Weinberg Equilibrium. Additionally,
+ WASP can retrieve and format data for other software programs such as the
+ Graphical Representation of Relationships (GRR) program, or STRUCTURE,
+ and depending on the nature of the samples and the depth of examination
+ the user desires to pursue. Beyond the quality control aspect of this
+ application, WASP can perform standard tests of association using the
+ Transmission Disequilibrium Test TDT for family-based datasets and the
+ chi-square test of association for case-control datasets.
+ .
+ We are also working on a graphical user interface (GUI) data manager
+ for PLATO called PLATO Viewer. This will allow you to do the exact
+ same things as the command line PLATO, however it will be more user
+ friendly by providing point and click batch setups as well as plotting
+ capabilities and data interaction.
+
+Package: plato-dbg
+Architecture: any
+Depends: ${misc:Depends}, plato (= ${binary:Version})
+Description: debug information for plato
+ plato is dominate by a single binary. This package adds debug
+ symbols to it.

Added: trunk/packages/plato/trunk/debian/copyright
===================================================================
--- trunk/packages/plato/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/plato/trunk/debian/copyright	2011-09-14 14:10:31 UTC (rev 7792)
@@ -0,0 +1,36 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: plato
+Source: <url://example.com>
+
+Files: *
+Copyright: <years> <put author's name and email here>
+           <years> <likewise for another author>
+License: <special license>
+ <Put the license of the package here indented by 1 space>
+ <This follows the format of Description: lines in control file>
+ .
+ <Including paragraphs>
+
+# If you want to use GPL v2 or later for the /debian/* files use 
+# the following clauses, or change it to suit. Delete these two lines
+Files: debian/*
+Copyright: 2011 Steffen Moeller <moeller at debian.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU 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 General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.

Added: trunk/packages/plato/trunk/debian/docs
===================================================================
Added: trunk/packages/plato/trunk/debian/plato.install
===================================================================
--- trunk/packages/plato/trunk/debian/plato.install	                        (rev 0)
+++ trunk/packages/plato/trunk/debian/plato.install	2011-09-14 14:10:31 UTC (rev 7792)
@@ -0,0 +1 @@
+plato	usr/bin

Added: trunk/packages/plato/trunk/debian/rules
===================================================================
--- trunk/packages/plato/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/plato/trunk/debian/rules	2011-09-14 14:10:31 UTC (rev 7792)
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+export DH_VERBOSE=1
+
+%:
+	dh $@ 
+
+
+override_dh_auto_test:
+	# do not test, missing cdblib.h
+
+override_dh_strip:
+	dh_strip --dbg-package plato-dbg
+
+VERSION=1.1
+get-orig-source:
+	[ -r ../plato-$(VERSION).tar.gz ] || wget -O ../plato-$(VERSION).tar.gz http://chgr.mc.vanderbilt.edu/ritchielab/software/builds/plato/plato-release$(VERSION).tar.gz
+	cd .. && tar xzf plato-$(VERSION).tar.gz
+	cd .. && mv plato-release plato-$(VERSION)
+	cd ../plato-$(VERSION) && make clean


Property changes on: trunk/packages/plato/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/plato/trunk/debian/source/format
===================================================================
--- trunk/packages/plato/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/plato/trunk/debian/source/format	2011-09-14 14:10:31 UTC (rev 7792)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/plato/trunk/debian/watch
===================================================================
--- trunk/packages/plato/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/plato/trunk/debian/watch	2011-09-14 14:10:31 UTC (rev 7792)
@@ -0,0 +1,2 @@
+version=3
+http://chgr.mc.vanderbilt.edu/ritchielab/software/builds/plato/plato-release([0-9.]+)\.tar\.gz


