[med-svn] [cgview] 02/02: initial packaging
Andreas Tille
tille at debian.org
Fri Nov 27 08:26:43 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository cgview.
commit c17c33e23d54564a401252d33a585d54244eeb34
Author: Andreas Tille <tille at debian.org>
Date: Fri Nov 27 09:23:29 2015 +0100
initial packaging
---
debian/changelog | 5 ++++
debian/compat | 1 +
debian/control | 60 ++++++++++++++++++++++++++++++++++++++++++++++++
debian/copyright | 29 +++++++++++++++++++++++
debian/rules | 22 ++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++
debian/watch | 3 +++
8 files changed, 133 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..17afb0a
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+cgview (0.0.20100111-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- DMPT <debian-med-packaging at lists.alioth.debian.org> Fri, 27 Nov 2015 09:06:21 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..24759c1
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,60 @@
+Source: cgview
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/cgview.git
+Vcs-Git: git://anonscm.debian.org/debian-med/cgview.git
+Homepage: http://wishart.biology.ualberta.ca/cgview/
+
+Package: cgview
+Architecture: any
+Depends: ${java:Depends},
+ ${misc:Depends}
+Description: Circular Genome Viewer
+ CGView is a Java package for generating high quality, zoomable maps of
+ circular genomes. Its primary purpose is to serve as a component of
+ sequence annotation pipelines, as a means of generating visual output
+ suitable for the web. Feature information and rendering options are
+ supplied to the program using an XML file, a tab delimited file, or an
+ NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG,
+ or Scalable Vector Graphics format), complete with labels, a title,
+ legends, and footnotes. In addition to the default full view map, the
+ program can generate a series of hyperlinked maps showing expanded
+ views. The linked maps can be explored using any web browser, allowing
+ rapid genome browsing, and facilitating data sharing. The feature labels
+ in maps can be hyperlinked to external resources, allowing CGView maps
+ to be integrated with existing web site content or databases.
+ .
+ In addition to the CGView application, an API is available for
+ generating maps from within other Java applications, using the
+ cgview package.
+ .
+ CGView can be used for any of the following:
+ * Bacterial genome visualization and browsing - CGView can be
+ incorporated into bacterial genome annotation pipelines, as a means
+ of generating web content for data visualization and navigation. The
+ PNG and image map content does not require Java applets or special
+ browser plugins.
+ * Genome poster generation - CGView can generate poster-sized images of
+ circular genomes in rasterized image formats or in Scalable Vector
+ Graphics format.
+ * Sequence analysis visualization - CGView can be used to display the
+ output of sequence analysis programs in a circular context.
+ .
+ CGView features:
+ * Images can be generated in PNG, JPG, or SVG format. See the
+ CGView gallery.
+ * Static or interactive maps can be generated. The interactive maps
+ make use of standard PNG images and HTML image maps. Scalable Vector
+ Graphics output is included in the interactive maps (see example).
+ * The XML input allows complete control over the appearance of the map.
+ * Tab delimited input files and NCBI ptt files can be used as an
+ alternative to the XML format.
+ * The CGView API can be used to incorporate CGView into Java
+ applications.
+ * The CGView applet can be used to incorporate zoomable maps into web
+ pages (see example).
+ * The CGView Server can be used to generate maps online.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..0a35c22
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: CGView
+Upstream-Contact: David S. Wishart <david.wishart at ualberta.ca>
+Source: http://wishart.biology.ualberta.ca/cgview/download.html
+Files-Excluded: */*.jar
+ */*.class
+ cgview/includes
+
+Files: *
+Copyright: 2004-2010 Paul Stothard
+License: GPL-2+
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: GPL-2+
+
+License: GPL-2+
+ This program is free software; you can redistribute it and/or 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 program 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.
+ .
+ On Debian systems you can find the full text of the GNU General Public
+ License version 2 (or later) at /usr/share/common-licenses/GPL-2.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..1d11ebc
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+%:
+ dh $@
+
+#get-orig-source:
+# . debian/get-orig-source
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..3f3d1de
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Paul Stothard and David S. Wishart
+ Title: Circular genome visualization and exploration using CGView
+ Journal: Bioinformatics
+ Year: 2004
+ Volume: 21
+ Number: 4
+ Pages: 537-539
+ DOI: 10.1093/bioinformatics/bti054
+ PMID: 15479716
+ URL: http://bioinformatics.oxfordjournals.org/content/21/4/537.short
+ eprint: http://bioinformatics.oxfordjournals.org/content/21/4/537.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..b5bdad9
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+# version=3
+# manually downloaded unversioned file from
+# http://wishart.biology.ualberta.ca/cgview/download.html
--
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