[med-svn] [seer] 12/13: Re-add debian/ dir
Andreas Tille
tille at debian.org
Thu Apr 14 09:49:56 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository seer.
commit 566f3de4d55aca0f5494157706e72022907a421c
Author: Andreas Tille <tille at debian.org>
Date: Thu Apr 14 11:47:13 2016 +0200
Re-add debian/ dir
---
debian/README.Debian | 12 +++++
debian/changelog | 11 ++++
debian/compat | 1 +
debian/control | 38 ++++++++++++++
debian/copyright | 26 ++++++++++
debian/examples | 1 +
debian/manpages | 1 +
debian/mans/blast_top_hits.1 | 28 ++++++++++
debian/mans/combineKmers.1 | 26 ++++++++++
debian/mans/filter_seer.1 | 41 +++++++++++++++
debian/mans/kmds.1 | 74 ++++++++++++++++++++++++++
debian/mans/map_back.1 | 26 ++++++++++
debian/mans/seer.1 | 75 +++++++++++++++++++++++++++
debian/patches/fix_lib_location.patch | 20 +++++++
debian/patches/hardening.patch | 39 ++++++++++++++
debian/patches/pthread_versus_hardening.patch | 20 +++++++
debian/patches/series | 3 ++
debian/rules | 21 ++++++++
debian/source/format | 1 +
debian/upstream/metadata | 8 +++
debian/watch | 3 ++
21 files changed, 475 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..144dcff
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,12 @@
+seer for Debian
+===============
+
+For more detailed documentation please see the seer Wiki page:
+
+ https://github.com/johnlees/seer/wiki/Usage
+
+There is also an example wrapper script in
+
+ examples/example_wrapper.py
+
+ -- Andreas Tille <tille at debian.org> Tue, 29 Mar 2016 19:32:29 +0200
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..bd6789a
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,11 @@
+seer (1.1.0-2) UNRELEASED; urgency=medium
+
+ * Suggests: fsm-lite
+
+ -- Andreas Tille <tille at debian.org> Tue, 12 Apr 2016 10:52:38 +0200
+
+seer (1.1.0-1) unstable; urgency=medium
+
+ * Initial release (Closes: #819674)
+
+ -- Andreas Tille <tille at debian.org> Thu, 31 Mar 2016 22:35:05 +0200
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..0de04bc
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,38 @@
+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-dev,
+# libhdf5-mpi-dev,
+ libgzstream-dev,
+ libboost-dev,
+ libboost-program-options-dev
+Standards-Version: 3.9.7
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/seer/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/seer/trunk/
+Homepage: https://github.com/johnlees/seer
+
+Package: seer
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ libtext-csv-perl
+Suggests: fsm-lite
+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.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..1c56362
--- /dev/null
+++ b/debian/copyright
@@ -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 John Lees <john at johnlees.me>
+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.
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..436566d
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1 @@
+example_wrapper.py
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..4f4649b
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*.1
diff --git a/debian/mans/blast_top_hits.1 b/debian/mans/blast_top_hits.1
new file mode 100644
index 0000000..15ce157
--- /dev/null
+++ b/debian/mans/blast_top_hits.1
@@ -0,0 +1,28 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH BLAST_TOP_HITS "1" "March 2016" "blast_top_hits 1.1.0" "User Commands"
+.SH NAME
+blast_top_hits \- reduces a blast or blat output file to the top hit for each query sequence only
+.SH SYNOPSIS
+.B blast_top_hits.pl
+\fI\,--input blast_out --mode blast <options>\/\fR
+.SH DESCRIPTION
+Reduces a blast or blat output file to the top hit for each query sequence only.
+.P
+This program belongs to seer(1) (Sequence Element (kmer) Enrichment Analysis).
+.SH OPTIONS
+.SS Required
+.TP
+\fB\-\-input\fR
+BLAST output file in \fB\-m\fR 6/\-outfmt 6 or BLAT .psl file
+.TP
+\fB\-\-mode\fR
+Either blast or blat
+.SS Optional
+.TP
+\fB\-\-full_query\fR
+The entire query must be reported as a match to appear in the output
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Shows this help.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/combineKmers.1 b/debian/mans/combineKmers.1
new file mode 100644
index 0000000..51aaa5a
--- /dev/null
+++ b/debian/mans/combineKmers.1
@@ -0,0 +1,26 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH COMBINEKMERS "1" "March 2016" "combineKmers 1.1.0" "User Commands"
+.SH NAME
+combineKmers \- basic algorithm to combine kmer counts across samples
+.P
+This program belongs to seer(1) (Sequence Element (kmer) Enrichment Analysis).
+.SH DESCRIPTION
+Basic algorithm to combine kmer counts across samples
+.SH OPTIONS
+.SS "Required options:"
+.TP
+\fB\-r\fR [ \fB\-\-samples\fR ] arg
+file with tab separated sample name and kmer file
+.TP
+\fB\-o\fR [ \fB\-\-output\fR ] arg
+output file prefix
+.SS "Other options:"
+.TP
+\fB\-\-min_samples\fR arg (=1)
+minimum number of samples kmer must occur in to be
+printed
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+full help message
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/filter_seer.1 b/debian/mans/filter_seer.1
new file mode 100644
index 0000000..f0c272b
--- /dev/null
+++ b/debian/mans/filter_seer.1
@@ -0,0 +1,41 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH FILTER_SEER "1" "March 2016" "filter_seer 1.1.0" "User Commands"
+.SH NAME
+filter_seer \- post filtering of significant kmers
+.SH DESCRIPTION
+Post filtering of significant kmers.
+.P
+This program belongs to seer(1) (Sequence Element (kmer) Enrichment Analysis).
+.SH OPTIONS
+.SS "Required options:"
+.TP
+\fB\-k\fR [ \fB\-\-kmers\fR ] arg
+file of output from seer
+.SS "Filtering options:"
+.TP
+\fB\-\-chisq\fR arg
+minimum unadjusted p\-value to output
+.TP
+\fB\-\-pval\fR arg
+minimum adjusted p\-value to output
+.TP
+\fB\-\-maf\fR arg
+minimum maf/max 1\-maf to output
+.TP
+\fB\-\-beta\fR arg
+minimum |beta| to output
+.TP
+\fB\-\-substr\fR
+remove smaller kmers completely represented elsewhere
+.TP
+\fB\-\-pos_beta\fR
+output positive effect sizes only
+.SS "Other options:"
+.TP
+\fB\-s\fR [ \fB\-\-sort\fR ] arg
+field to sort on: chisq, pval, maf or beta
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+full help message
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/kmds.1 b/debian/mans/kmds.1
new file mode 100644
index 0000000..c02e1c9
--- /dev/null
+++ b/debian/mans/kmds.1
@@ -0,0 +1,74 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH KMDS "1" "March 2016" "kmds 1.1.0" "User Commands"
+.SH NAME
+kmds \- control for population structure
+.SH DESCRIPTION
+Control for population structure. Filter kmers and create a matrix representing population structure.
+.P
+This program belongs to seer(1) (Sequence Element (kmer) Enrichment Analysis).
+.SH OPTIONS
+1) filter and subsample with \fB\-\-no_mds\fR and \fB\-\-size\fR
+.P
+2) combine, and do metric multidimensional scaling with \fB\-\-combine_mds\fR
+.SS "Required options:"
+.TP
+\fB\-k\fR [ \fB\-\-kmers\fR ] arg
+dsm kmer output file
+.TP
+\fB\-p\fR [ \fB\-\-pheno\fR ] arg
+\&.pheno metadata
+.SS "MDS options:"
+.TP
+\fB\-o\fR [ \fB\-\-output\fR ] arg
+output prefix for new dsm file
+.TP
+\fB\-\-no_mds\fR
+do not perform MDS; output subsampled matrix instead
+.TP
+\fB\-\-write_distances\fR
+write csv of distance matrix
+.TP
+\fB\-\-mds_concat\fR arg
+list of subsampled matrices to use in MDS. Performs
+only MDS; implies \fB\-\-no_filtering\fR
+.TP
+\fB\-\-pc\fR arg (=3)
+number of principal coordinates to output
+.TP
+\fB\-\-size\fR arg (=1000000)
+number of kmers to use in MDS
+.TP
+\fB\-\-threads\fR arg (=1)
+number of threads. Suggested: 4
+.SS "Filtering options:"
+.TP
+\fB\-\-no_filtering\fR
+turn off all filtering and do not output new kmer
+file
+.TP
+\fB\-\-max_length\fR arg (=100)
+maximum kmer length
+.TP
+\fB\-\-maf\fR arg (=0.01)
+minimum kmer frequency
+.TP
+\fB\-\-min_words\fR arg
+minimum kmer occurrences. Overrides \fB\-\-maf\fR
+.TP
+\fB\-\-chisq\fR arg (=10e\-5)
+p\-value threshold for initial chi squared test. Set
+to 1 to show all
+.SS "Other options:"
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+full help message
+.SH EXAMPLE
+Filter kmers and create a matrix representing population structure with kmds
+.IP
+kmds -k dsm_input.txt.gz --pheno metadata.pheno -o filtered
+.P
+To spread this process out, run the following command on each dsm file
+.IP
+kmds -k dsm_input.txt.gz --pheno metadata.pheno --no_mds --size 10000
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/map_back.1 b/debian/mans/map_back.1
new file mode 100644
index 0000000..ca1c85a
--- /dev/null
+++ b/debian/mans/map_back.1
@@ -0,0 +1,26 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH MAP_BACK "1" "March 2016" "map_back 1.1.0" "User Commands"
+.SH NAME
+map_back \- context of significant kmers
+.SH DESCRIPTION
+Context of significant kmers.
+.P
+This program belongs to seer(1) (Sequence Element (kmer) Enrichment Analysis).
+.SH OPTIONS
+.SS "Required options:"
+.TP
+\fB\-k\fR [ \fB\-\-kmers\fR ] arg
+seer kmer output file
+.TP
+\fB\-r\fR [ \fB\-\-references\fR ] arg
+file with tab separated reference name and fasta
+file
+.SS "Other options:"
+.TP
+\fB\-\-threads\fR arg (=1)
+number of threads. Suggested: 4
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+full help message
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/seer.1 b/debian/mans/seer.1
new file mode 100644
index 0000000..888a132
--- /dev/null
+++ b/debian/mans/seer.1
@@ -0,0 +1,75 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3.
+.TH SEER "1" "March 2016" "seer 1.1.0" "User Commands"
+.SH NAME
+seer \- sequence element enrichment analysis
+.SH DESCRIPTION
+Sequence Element Enrichment Analysis
+.P
+The .pheno file format is tab separated, two columns with sample name, one with phenotype. Phenotypes of only 0 or 1 will be treated as binary, any other value and the phenotype will be treated as quantitative. Therefore for missing phenotype values the sample should simply be excluded from this file.
+.SH OPTIONS
+.SS "Required options:"
+.TP
+\fB\-k\fR [ \fB\-\-kmers\fR ] arg
+dsm kmer output file
+.TP
+\fB\-p\fR [ \fB\-\-pheno\fR ] arg
+\&.pheno metadata
+.SS "Covariate options:"
+.TP
+\fB\-\-struct\fR arg
+mds values from kmds
+.TP
+\fB\-\-covar_file\fR arg
+file containing covariates
+.TP
+\fB\-\-covar_list\fR arg
+list of columns covariates to use. Format is 1,2q,3
+(use q for quantitative)
+.SS "Performance options:"
+.TP
+\fB\-\-threads\fR arg (=1)
+number of threads. Suggested: 4
+.SS "Filtering options:"
+.TP
+\fB\-\-no_filtering\fR
+turn off all filtering and peform tests on all kmers
+input
+.TP
+\fB\-\-max_length\fR arg (=100)
+maximum kmer length
+.TP
+\fB\-\-maf\fR arg (=0.01)
+minimum kmer frequency
+.TP
+\fB\-\-min_words\fR arg
+minimum kmer occurrences. Overrides \fB\-\-maf\fR
+.TP
+\fB\-\-positive_only\fR
+only test words with a predicted positive effect
+direction
+.TP
+\fB\-\-chisq\fR arg (=10e\-5)
+p\-value threshold for initial chi squared test. Set
+to 1 to show all
+.TP
+\fB\-\-pval\fR arg (=10e\-8)
+p\-value threshold for final logistic test. Set to 1
+to show all
+.SS "Other options:"
+.TP
+\fB\-\-print_samples\fR
+print lists of samples significant kmers were found
+in
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+full help message
+.SH EXAMPLES
+Basic usage:
+.IP
+seer -k dsm_input.txt.gz --pheno metadata.pheno > significant_kmers.txt
+.P
+To use the kmds output, increase execution speed and give the most complete output
+.IP
+seer -k filtered.gz --pheno metadata.pheno --struct filtered.dsm --threads 4 --print_samples
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/patches/fix_lib_location.patch b/debian/patches/fix_lib_location.patch
new file mode 100644
index 0000000..e27b273
--- /dev/null
+++ b/debian/patches/fix_lib_location.patch
@@ -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$(PREFIX)/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
new file mode 100644
index 0000000..a667367
--- /dev/null
+++ b/debian/patches/hardening.patch
@@ -0,0 +1,39 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 29 Mar 2016 19:32:29 +0200
+Description: Propagate hardening options
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -13,11 +13,11 @@ BINDIR=$(PREFIX)/bin
+ # gcc
+ 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=-lgzstream -lz -lboost_program_options
+-FILTER_LDLIBS=-L$(PREFIX)/lib -lboost_program_options
++MAP_LDLIBS=-lboost_program_options $(LDFLAGS)
++COMBINE_LDLIBS=-lgzstream -lz -lboost_program_options $(LDFLAGS)
++FILTER_LDLIBS=-lboost_program_options $(LDFLAGS)
+
+-CPPFLAGS=-I$(PREFIX)/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1
++CPPFLAGS+=-I$(PREFIX)/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1
+
+ # For static linking. To use type 'make static'
+ # Requires icpc and mkl
+@@ -56,13 +56,13 @@ kmds: $(KMDS_OBJECTS)
+ $(LINK.cpp) $^ $(SEER_LDLIBS) -o $@
+
+ map_back: $(MAP_OBJECTS)
+- $(LINK.cpp) $^ $(MAP_LDLIBS) -o $@
++ $(LINK.cpp) $^ $(MAP_LDLIBS) $(LDFLAGS) -o $@
+
+ combineKmers: $(COMBINE_OBJECTS)
+- $(LINK.cpp) $^ $(COMBINE_LDLIBS) -o $@
++ $(LINK.cpp) $^ $(COMBINE_LDLIBS) $(LDFLAGS) -o $@
+
+ filter_seer: $(FILTER_OBJECTS)
+- $(LINK.cpp) $^ $(FILTER_LDLIBS) -o $@
++ $(LINK.cpp) $^ $(FILTER_LDLIBS) $(LDFLAGS) -o $@
+
+ seer_static: $(SEER_OBJECTS)
+ $(LINK.cpp) $^ $(SEER_STATIC_LDLIBS) -o $@
diff --git a/debian/patches/pthread_versus_hardening.patch b/debian/patches/pthread_versus_hardening.patch
new file mode 100644
index 0000000..e0864a4
--- /dev/null
+++ b/debian/patches/pthread_versus_hardening.patch
@@ -0,0 +1,20 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 29 Mar 2016 19:32:29 +0200
+Description: Set -pthread inside Makefile
+ When doing this in debian/rules via
+ export LDFLAGS := -pthread $(LDFLAGS)
+ the hardening options are overriden
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -12,8 +12,8 @@ BINDIR=$(PREFIX)/bin
+ #FILTER_LDLIBS=-L$(PREFIX)/lib -lboost_program_options -mkl
+ # gcc
+ CXXFLAGS+=-Wall -O3 -std=c++11
+-SEER_LDLIBS=-lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas $(LDFLAGS)
+-MAP_LDLIBS=-lboost_program_options $(LDFLAGS)
++SEER_LDLIBS=-lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas -pthread $(LDFLAGS)
++MAP_LDLIBS=-lboost_program_options -pthread $(LDFLAGS)
+ COMBINE_LDLIBS=-lgzstream -lz -lboost_program_options $(LDFLAGS)
+ FILTER_LDLIBS=-lboost_program_options $(LDFLAGS)
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..9762ec0
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+fix_lib_location.patch
+hardening.patch
+pthread_versus_hardening.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..46ddc59
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,21 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+
+include /usr/share/dpkg/architecture.mk
+export CPATH := /usr/include/hdf5/serial
+export LIBRARY_PATH := /usr/lib/$(DEB_TARGET_MULTIARCH)/hdf5/serial
+
+## The following destroys hardening flags.
+## --> see debian/patches/pthread_versus_hardening.patch
+##export LDFLAGS := -pthread $(LDFLAGS)
+
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+override_dh_auto_install:
+ dh_auto_install -- PREFIX=$(CURDIR)/debian/$(DEBPKGNAME)/usr
+ cp -a scripts/blast_top_hits.pl $(CURDIR)/debian/$(DEBPKGNAME)/usr/bin/blast_top_hits
+
+%:
+ dh $@
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..848f276
--- /dev/null
+++ b/debian/upstream/metadata
@@ -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
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..01bbc15
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/johnlees/seer/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seer.git
More information about the debian-med-commit
mailing list