[med-svn] r21390 - in trunk/packages: . plast plast/trunk plast/trunk/debian plast/trunk/debian/patches plast/trunk/debian/source plast/trunk/debian/upstream
Andreas Tille
tille at moszumanska.debian.org
Tue Feb 9 09:29:22 UTC 2016
Author: tille
Date: 2016-02-09 09:29:21 +0000 (Tue, 09 Feb 2016)
New Revision: 21390
Added:
trunk/packages/plast/
trunk/packages/plast/trunk/
trunk/packages/plast/trunk/debian/
trunk/packages/plast/trunk/debian/changelog
trunk/packages/plast/trunk/debian/compat
trunk/packages/plast/trunk/debian/control
trunk/packages/plast/trunk/debian/copyright
trunk/packages/plast/trunk/debian/patches/
trunk/packages/plast/trunk/debian/patches/fix_format_string.patch
trunk/packages/plast/trunk/debian/patches/series
trunk/packages/plast/trunk/debian/rules
trunk/packages/plast/trunk/debian/source/
trunk/packages/plast/trunk/debian/source/format
trunk/packages/plast/trunk/debian/upstream/
trunk/packages/plast/trunk/debian/upstream/metadata
trunk/packages/plast/trunk/debian/watch
Log:
Inject plast
Added: trunk/packages/plast/trunk/debian/changelog
===================================================================
--- trunk/packages/plast/trunk/debian/changelog (rev 0)
+++ trunk/packages/plast/trunk/debian/changelog 2016-02-09 09:29:21 UTC (rev 21390)
@@ -0,0 +1,5 @@
+plast (2.3.1-2) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 09 Feb 2016 10:20:36 +0100
Added: trunk/packages/plast/trunk/debian/compat
===================================================================
--- trunk/packages/plast/trunk/debian/compat (rev 0)
+++ trunk/packages/plast/trunk/debian/compat 2016-02-09 09:29:21 UTC (rev 21390)
@@ -0,0 +1 @@
+9
Added: trunk/packages/plast/trunk/debian/control
===================================================================
--- trunk/packages/plast/trunk/debian/control (rev 0)
+++ trunk/packages/plast/trunk/debian/control 2016-02-09 09:29:21 UTC (rev 21390)
@@ -0,0 +1,26 @@
+Source: plast
+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),
+ cmake,
+ default-jdk
+Standards-Version: 3.9.7
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/plast/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/plast/trunk/
+Homepage: https://plast.inria.fr/
+
+Package: plast
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: Parallel Local Sequence Alignment Search Tool
+ PLAST is a fast, accurate and NGS scalable bank-to-bank sequence
+ similarity search tool providing significant accelerations of seeds-
+ based heuristic comparison methods, such as the Blast suite of
+ algorithms.
+ .
+ Relying on unique software architecture, PLAST takes full advantage of
+ recent multi-core personal computers without requiring any additional
+ hardware devices.
Added: trunk/packages/plast/trunk/debian/copyright
===================================================================
--- trunk/packages/plast/trunk/debian/copyright (rev 0)
+++ trunk/packages/plast/trunk/debian/copyright 2016-02-09 09:29:21 UTC (rev 21390)
@@ -0,0 +1,11 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: <pkg>
+Source: <path_to_download>
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: © 2014 maintainername <maintainer at e.mail>
+License: <license>
Added: trunk/packages/plast/trunk/debian/patches/fix_format_string.patch
===================================================================
--- trunk/packages/plast/trunk/debian/patches/fix_format_string.patch (rev 0)
+++ trunk/packages/plast/trunk/debian/patches/fix_format_string.patch 2016-02-09 09:29:21 UTC (rev 21390)
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 09 Feb 2016 10:20:36 +0100
+Description: Fix for more picky gcc-5
+
+--- a/src/tools/PlastCmd.cpp
++++ b/src/tools/PlastCmd.cpp
+@@ -159,7 +159,7 @@ int main (int argc, char* argv[])
+ }
+ catch (...)
+ {
+- fprintf (stderr, MSG_MAIN_MSG4);
++ fprintf (stderr, "%s", MSG_MAIN_MSG4);
+ }
+
+ return 0;
Added: trunk/packages/plast/trunk/debian/patches/series
===================================================================
--- trunk/packages/plast/trunk/debian/patches/series (rev 0)
+++ trunk/packages/plast/trunk/debian/patches/series 2016-02-09 09:29:21 UTC (rev 21390)
@@ -0,0 +1 @@
+fix_format_string.patch
Added: trunk/packages/plast/trunk/debian/rules
===================================================================
--- trunk/packages/plast/trunk/debian/rules (rev 0)
+++ trunk/packages/plast/trunk/debian/rules 2016-02-09 09:29:21 UTC (rev 21390)
@@ -0,0 +1,20 @@
+#!/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 $@ --buildsystem=cmake
+
Property changes on: trunk/packages/plast/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/plast/trunk/debian/source/format
===================================================================
--- trunk/packages/plast/trunk/debian/source/format (rev 0)
+++ trunk/packages/plast/trunk/debian/source/format 2016-02-09 09:29:21 UTC (rev 21390)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/plast/trunk/debian/upstream/metadata
===================================================================
--- trunk/packages/plast/trunk/debian/upstream/metadata (rev 0)
+++ trunk/packages/plast/trunk/debian/upstream/metadata 2016-02-09 09:29:21 UTC (rev 21390)
@@ -0,0 +1,11 @@
+Reference:
+ Author: Van Hoa Nguyen and Dominique Lavenier
+ Title: "PLAST: parallel local alignment search tool for database comparison"
+ Journal: BMC Bioinformatics
+ Year: 2009
+ Volume: 10
+ Pages: 329
+ DOI: 10.1186/1471-2105-10-329
+ PMID: 19821978
+ URL: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-329
+ eprint: http://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-10-329?site=bmcbioinformatics.biomedcentral.com
Added: trunk/packages/plast/trunk/debian/watch
===================================================================
--- trunk/packages/plast/trunk/debian/watch (rev 0)
+++ trunk/packages/plast/trunk/debian/watch 2016-02-09 09:29:21 UTC (rev 21390)
@@ -0,0 +1,3 @@
+version=3
+
+https://plast.inria.fr/developer-guide/ .*/files/plast_source_v(\d[\d.]+)\.tar\.gz
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