[med-svn] r16001 - in trunk/packages: . spades spades/trunk spades/trunk/debian spades/trunk/debian/source
Andreas Tille
tille at moszumanska.debian.org
Wed Feb 5 14:39:00 UTC 2014
Author: tille
Date: 2014-02-05 14:39:00 +0000 (Wed, 05 Feb 2014)
New Revision: 16001
Added:
trunk/packages/spades/
trunk/packages/spades/trunk/
trunk/packages/spades/trunk/debian/
trunk/packages/spades/trunk/debian/changelog
trunk/packages/spades/trunk/debian/compat
trunk/packages/spades/trunk/debian/control
trunk/packages/spades/trunk/debian/copyright
trunk/packages/spades/trunk/debian/rules
trunk/packages/spades/trunk/debian/source/
trunk/packages/spades/trunk/debian/source/format
trunk/packages/spades/trunk/debian/upstream
trunk/packages/spades/trunk/debian/watch
Log:
Inject initial (not yet working) packaging for spades
Added: trunk/packages/spades/trunk/debian/changelog
===================================================================
--- trunk/packages/spades/trunk/debian/changelog (rev 0)
+++ trunk/packages/spades/trunk/debian/changelog 2014-02-05 14:39:00 UTC (rev 16001)
@@ -0,0 +1,5 @@
+spades (3.0.0-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Wed, 05 Feb 2014 15:12:36 +0100
Added: trunk/packages/spades/trunk/debian/compat
===================================================================
--- trunk/packages/spades/trunk/debian/compat (rev 0)
+++ trunk/packages/spades/trunk/debian/compat 2014-02-05 14:39:00 UTC (rev 16001)
@@ -0,0 +1 @@
+9
Added: trunk/packages/spades/trunk/debian/control
===================================================================
--- trunk/packages/spades/trunk/debian/control (rev 0)
+++ trunk/packages/spades/trunk/debian/control 2014-02-05 14:39:00 UTC (rev 16001)
@@ -0,0 +1,20 @@
+Source: spades
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/spades/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/spades/trunk/
+Homepage: http://bioinf.spbau.ru/en/spades
+
+Package: spades
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: genome assembler for single-cell and isolates data sets
+ The SPAdes – St. Petersburg genome assembler is intended for both
+ standard isolates and single-cell MDA bacteria assemblies. It works
+ with Illumina or IonTorrent reads and is capable of providing hybrid
+ assemblies using PacBio and Sanger reads. You can also provide
+ additional contigs that will be used as long reads.
Added: trunk/packages/spades/trunk/debian/copyright
===================================================================
--- trunk/packages/spades/trunk/debian/copyright (rev 0)
+++ trunk/packages/spades/trunk/debian/copyright 2014-02-05 14:39:00 UTC (rev 16001)
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SPAdes
+Source: http://spades.bioinf.spbau.ru/
+
+Files: *
+Copyright: © 2011-2013 Saint-Petersburg Academic University
+License: GPLv2+
+
+Files: debian/*
+Copyright: © 2014 Andreas Tille <tille at debian.org>
+License: GPLv2+
+
+License: GPLv2+
+ This program 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 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.
+ .
+ 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.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ .
+ On Debian systems you can find the full test of the GNU General Public
+ License version 2 at /usr/share/common-licenses/GPL-2.
Added: trunk/packages/spades/trunk/debian/rules
===================================================================
--- trunk/packages/spades/trunk/debian/rules (rev 0)
+++ trunk/packages/spades/trunk/debian/rules 2014-02-05 14:39:00 UTC (rev 16001)
@@ -0,0 +1,23 @@
+#!/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/cdbs/1/rules/buildvars.mk
+# and use what is set there. Any hint whether dh might set variables in
+# a similar manner are welcome.
+
+%:
+ dh $@
+
+#get-orig-source:
+# . debian/get-orig-source
Property changes on: trunk/packages/spades/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/spades/trunk/debian/source/format
===================================================================
--- trunk/packages/spades/trunk/debian/source/format (rev 0)
+++ trunk/packages/spades/trunk/debian/source/format 2014-02-05 14:39:00 UTC (rev 16001)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/spades/trunk/debian/upstream
===================================================================
--- trunk/packages/spades/trunk/debian/upstream (rev 0)
+++ trunk/packages/spades/trunk/debian/upstream 2014-02-05 14:39:00 UTC (rev 16001)
@@ -0,0 +1,21 @@
+Reference:
+ - Author: Anton Bankevich and Sergey Nurk and Dmitry Antipov and Alexey A. Gurevich and Mikhail Dvorkin and Alexander S. Kulikov and Valery M. Lesin and Sergey I. Nikolenko and Son Pham and Andrey D. Prjibelski and Alexey V. Pyshkin and Alexander V. Sirotkin and Nikolay Vyahhi and Glenn Tesler and Max A. Alekseyev and Pavel A. Pevzner
+ Title: "SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing"
+ Journal: Journal of Computational Biology
+ Year: 2012
+ Volume: 19
+ Number: 5
+ Pages: 455-477
+ DOI: 10.1089/cmb.2012.0021
+ PMID: 22506599
+ URL: http://online.liebertpub.com/doi/abs/10.1089/cmb.2012.0021
+ eprint: http://online.liebertpub.com/doi/pdfplus/10.1089/cmb.2012.0021
+ - Author: Sergey Nurk and Anton Bankevich and Dmitry Antipov and Alexey Gurevich and Anton Korobeynikov and Alla Lapidus and Andrey Prjibelsky and Alexey Pyshkin and Alexander Sirotkin and Yakov Sirotkin and Ramunas Stepanauskas and Jeffrey McLean and Roger Lasken and Scott Clingenpeel and Tanja Woyke and Glenn Tesler and Max Alekseyev and Pavel Pevzner
+ Title: Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads
+ Journal: Lecture Notes in Computer Science
+ Year: 2013
+ Volume: 7821
+ Pages: 158-170
+ DOI: 10.1007/978-3-642-37195-0_13
+ URL: http://link.springer.com/chapter/10.1007%2F978-3-642-37195-0_13
+
Added: trunk/packages/spades/trunk/debian/watch
===================================================================
--- trunk/packages/spades/trunk/debian/watch (rev 0)
+++ trunk/packages/spades/trunk/debian/watch 2014-02-05 14:39:00 UTC (rev 16001)
@@ -0,0 +1,6 @@
+version=3
+# does not work yet
+#opts=downloadurlmangle=s/release($([\d.]+)\//&SPAdes-$1.tar.gz/ \
+# http://spades.bioinf.spbau.ru/release([\d.]+)/
+#
+# http://spades.bioinf.spbau.ru/release3.0.0/SPAdes-3.0.0.tar.gz
\ No newline at end of file
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