[med-svn] r21621 - in trunk/packages: . seer seer/trunk seer/trunk/debian seer/trunk/debian/patches seer/trunk/debian/source seer/trunk/debian/upstream
Andreas Tille
tille at moszumanska.debian.org
Tue Mar 29 19:12:26 UTC 2016
Author: tille
Date: 2016-03-29 19:12:26 +0000 (Tue, 29 Mar 2016)
New Revision: 21621
Added:
trunk/packages/seer/
trunk/packages/seer/trunk/
trunk/packages/seer/trunk/debian/
trunk/packages/seer/trunk/debian/changelog
trunk/packages/seer/trunk/debian/compat
trunk/packages/seer/trunk/debian/control
trunk/packages/seer/trunk/debian/copyright
trunk/packages/seer/trunk/debian/patches/
trunk/packages/seer/trunk/debian/patches/fix_lib_location.patch
trunk/packages/seer/trunk/debian/patches/series
trunk/packages/seer/trunk/debian/rules
trunk/packages/seer/trunk/debian/source/
trunk/packages/seer/trunk/debian/source/format
trunk/packages/seer/trunk/debian/upstream/
trunk/packages/seer/trunk/debian/upstream/metadata
trunk/packages/seer/trunk/debian/watch
Log:
Inject seer
Added: trunk/packages/seer/trunk/debian/changelog
===================================================================
--- trunk/packages/seer/trunk/debian/changelog (rev 0)
+++ trunk/packages/seer/trunk/debian/changelog 2016-03-29 19:12:26 UTC (rev 21621)
@@ -0,0 +1,5 @@
+seer (1.1.0-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 29 Mar 2016 19:32:29 +0200
Added: trunk/packages/seer/trunk/debian/compat
===================================================================
--- trunk/packages/seer/trunk/debian/compat (rev 0)
+++ trunk/packages/seer/trunk/debian/compat 2016-03-29 19:12:26 UTC (rev 21621)
@@ -0,0 +1 @@
+9
Added: trunk/packages/seer/trunk/debian/control
===================================================================
--- trunk/packages/seer/trunk/debian/control (rev 0)
+++ trunk/packages/seer/trunk/debian/control 2016-03-29 19:12:26 UTC (rev 21621)
@@ -0,0 +1,35 @@
+Source: seer
+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),
+ libarmadillo-dev,
+ libdlib-dev,
+ libhdf5-mpi-dev | libhdf5-dev,
+ libxdmf-dev,
+ libboost-dev
+Standards-Version: 3.9.7
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/seer/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/seer/trunk/
+Homepage: <homepage>
+
+Package: seer
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: genomic sequence element (kmer) enrichment analysis
+ Bacterial genomes vary extensively in terms of both gene content and
+ gene sequence - this plasticity hampers the use of traditional SNP-based
+ methods for identifying all genetic associations with phenotypic
+ variation. SEER provides a computationally scalable and widely
+ applicable statistical method for the identification of sequence
+ elements that are significantly enriched in a phenotype of interest.
+ SEER is applicable to even tens of thousands of genomes by counting variable-
+ length k-mers using a distributed string-mining algorithm. Robust
+ options are provided for association analysis that also correct for the
+ clonal population structure of bacteria. Using large collections of
+ genomes of the major human pathogen Streptococcus pneumoniae, SEER
+ identifies relevant previously characterised resistance determinants for
+ several antibiotics. We thus demonstrate that our method can answer
+ important biologically and medically relevant questions.
Added: trunk/packages/seer/trunk/debian/copyright
===================================================================
--- trunk/packages/seer/trunk/debian/copyright (rev 0)
+++ trunk/packages/seer/trunk/debian/copyright 2016-03-29 19:12:26 UTC (rev 21621)
@@ -0,0 +1,26 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: John Lees <john at johnlees.me>
+Upstream-Name: seer
+Source: https://github.com/johnlees/seer/releases
+
+Files: *
+Copyright: 2015-2016 <upstream>
+License: GPL-2+
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: GPL-2+
+
+License: GPL-2+
+ 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.
+ .
+ On Debian systems you can find a copy of the GNU General Public License
+ version 2 or later at /usr/share/common-licenses/GPL-2.
Added: trunk/packages/seer/trunk/debian/patches/fix_lib_location.patch
===================================================================
--- trunk/packages/seer/trunk/debian/patches/fix_lib_location.patch (rev 0)
+++ trunk/packages/seer/trunk/debian/patches/fix_lib_location.patch 2016-03-29 19:12:26 UTC (rev 21621)
@@ -0,0 +1,20 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 29 Mar 2016 19:32:29 +0200
+Description: Remove non-existing library pathes
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -11,10 +11,10 @@ BINDIR=$(PREFIX)/bin
+ #COMBINE_LDLIBS=-L../gzstream -L$(PREFIX)/lib -lgzstream -lz -lboost_program_options
+ #FILTER_LDLIBS=-L$(PREFIX)/lib -lboost_program_options -mkl
+ # gcc
+-CXXFLAGS=-Wall -O3 -std=c++11
+-SEER_LDLIBS=-L../gzstream -L$(PREFIX)/lib -lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas
++CXXFLAGS+=-Wall -O3 -std=c++11
++SEER_LDLIBS=-lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas $(LDFLAGS)
+ MAP_LDLIBS=-L$(PREFIX)/lib -lboost_program_options
+-COMBINE_LDLIBS=-L../gzstream -L$(PREFIX)/lib -lgzstream -lz -lboost_program_options
++COMBINE_LDLIBS=-lgzstream -lz -lboost_program_options
+ FILTER_LDLIBS=-L$(PREFIX)/lib -lboost_program_options
+
+ CPPFLAGS=-I$(PREFIX)/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1
Added: trunk/packages/seer/trunk/debian/patches/series
===================================================================
--- trunk/packages/seer/trunk/debian/patches/series (rev 0)
+++ trunk/packages/seer/trunk/debian/patches/series 2016-03-29 19:12:26 UTC (rev 21621)
@@ -0,0 +1 @@
+fix_lib_location.patch
Added: trunk/packages/seer/trunk/debian/rules
===================================================================
--- trunk/packages/seer/trunk/debian/rules (rev 0)
+++ trunk/packages/seer/trunk/debian/rules 2016-03-29 19:12:26 UTC (rev 21621)
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+ dh $@
Property changes on: trunk/packages/seer/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/seer/trunk/debian/source/format
===================================================================
--- trunk/packages/seer/trunk/debian/source/format (rev 0)
+++ trunk/packages/seer/trunk/debian/source/format 2016-03-29 19:12:26 UTC (rev 21621)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/seer/trunk/debian/upstream/metadata
===================================================================
--- trunk/packages/seer/trunk/debian/upstream/metadata (rev 0)
+++ trunk/packages/seer/trunk/debian/upstream/metadata 2016-03-29 19:12:26 UTC (rev 21621)
@@ -0,0 +1,8 @@
+Reference:
+ Author: John A Lees and Minna Vehkala and Niko Välimäki and Simon R Harris and Claire Chewapreecha and Nicholas J Croucher and Pekka Marttinen and Mark R Davies and Andrew C Steer and Stephen Y C Tong and Antti Honkela and Julian Parkhill and Stephen D Bentley and Jukka Corander
+ Title: Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
+ Journal: bioRxiv
+ Year: 2016
+ DOI: 10.1101/038463
+ URL: http://biorxiv.org/content/biorxiv/early/2016/03/02/038463
+ eprint: http://biorxiv.org/content/biorxiv/early/2016/03/02/038463.full.pdf
Added: trunk/packages/seer/trunk/debian/watch
===================================================================
--- trunk/packages/seer/trunk/debian/watch (rev 0)
+++ trunk/packages/seer/trunk/debian/watch 2016-03-29 19:12:26 UTC (rev 21621)
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/johnlees/seer/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
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