[med-svn] [pirs] 02/02: Debian packaging, Attention: The source contains two non-distributable files. This needs to be clarified.
Andreas Tille
tille at debian.org
Tue Aug 2 14:45:14 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository pirs.
commit 095277884be92ef97fea0a443b3077474ef3f852
Author: Andreas Tille <tille at debian.org>
Date: Tue Aug 2 16:43:41 2016 +0200
Debian packaging, Attention: The source contains two non-distributable files. This needs to be clarified.
---
debian/changelog | 5 +
debian/clean | 18 +++
debian/compat | 1 +
debian/control | 86 +++++++++++
debian/copyright | 166 +++++++++++++++++++++
debian/patches/series | 1 +
.../patches/use_debian_packaged_libgzstream.patch | 69 +++++++++
debian/pirs-examples.install | 2 +
debian/pirs-profiles.install | 1 +
debian/pirs-profiles.lintian-overrides | 2 +
debian/pirs.docs | 1 +
debian/pirs.install | 2 +
debian/rules | 68 +++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++
debian/watch | 4 +
16 files changed, 439 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..5a0c773
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+pirs (1.11+dfsg-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 02 Aug 2016 12:12:20 +0200
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..9282e75
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1,18 @@
+src/pirs/Makefile.in
+src/pirs/src/Makefile.in
+src/pirs/aclocal.m4
+src/pirs/config.h*
+src/pirs/compile
+src/pirs/configure
+src/pirs/depcomp
+src/pirs/install-sh
+src/pirs/missing
+src/stator/gcContCvgBias/Makefile.in
+src/stator/gcContCvgBias/aclocal.m4
+src/stator/gcContCvgBias/compile
+src/stator/gcContCvgBias/config.h.in
+src/stator/gcContCvgBias/configure
+src/stator/gcContCvgBias/depcomp
+src/stator/gcContCvgBias/install-sh
+src/stator/gcContCvgBias/missing
+src/stator/gcContCvgBias/src/Makefile.in
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..b200171
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,86 @@
+Source: pirs
+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),
+ dh-autoreconf,
+ libboost-dev,
+ zlib1g-dev,
+ libgzstream-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ppirs.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/pirs.git
+Homepage: ftp://ftp.genomics.org.cn/pub/pIRS/ReadMe.txt
+
+Package: pirs
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ pirs-profiles
+Description: profile basd Illumina pair-end Reads Simulator
+ The program pIRS can be used for simulating Illumina PE reads, with a
+ series of characters generated by Illumina sequencing platform, such as
+ insert size distribution, sequencing error(substitution, insertion,
+ deletion), quality score and GC content-coverage bias.
+ .
+ The insert size follows a normal distribution, so users should set the
+ mean value and standard deviation. Usually the standard deviation is set
+ as 1/20 of the mean value. The normal distribution by Box-Muller method
+ is simulated.
+ .
+ The program simulates sequencing error, quality score and GC content-
+ coverage bias according to the empirical distribution profile. Some
+ default profiles counted from lots of real sequencing data are provided.
+ .
+ To simulate reads from diploid genome, users should simulate the diploid
+ genome sequence firstly by setting the ratio of heterozygosis SNP,
+ heterozygosis InDel and structure variation.
+
+Package: pirs-profiles
+Architecture: all
+Depends: ${misc:Depends}
+Description: profile basd Illumina pair-end Reads Simulator (profile data)
+ The program pIRS can be used for simulating Illumina PE reads, with a
+ series of characters generated by Illumina sequencing platform, such as
+ insert size distribution, sequencing error(substitution, insertion,
+ deletion), quality score and GC content-coverage bias.
+ .
+ The insert size follows a normal distribution, so users should set the
+ mean value and standard deviation. Usually the standard deviation is set
+ as 1/20 of the mean value. The normal distribution by Box-Muller method
+ is simulated.
+ .
+ The program simulates sequencing error, quality score and GC content-
+ coverage bias according to the empirical distribution profile. Some
+ default profiles counted from lots of real sequencing data are provided.
+ .
+ To simulate reads from diploid genome, users should simulate the diploid
+ genome sequence firstly by setting the ratio of heterozygosis SNP,
+ heterozygosis InDel and structure variation.
+ .
+ This package contains the profile data.
+
+Package: pirs-examples
+Architecture: all
+Depends: ${misc:Depends}
+Description: profile basd Illumina pair-end Reads Simulator (example data)
+ The program pIRS can be used for simulating Illumina PE reads, with a
+ series of characters generated by Illumina sequencing platform, such as
+ insert size distribution, sequencing error(substitution, insertion,
+ deletion), quality score and GC content-coverage bias.
+ .
+ The insert size follows a normal distribution, so users should set the
+ mean value and standard deviation. Usually the standard deviation is set
+ as 1/20 of the mean value. The normal distribution by Box-Muller method
+ is simulated.
+ .
+ The program simulates sequencing error, quality score and GC content-
+ coverage bias according to the empirical distribution profile. Some
+ default profiles counted from lots of real sequencing data are provided.
+ .
+ To simulate reads from diploid genome, users should simulate the diploid
+ genome sequence firstly by setting the ratio of heterozygosis SNP,
+ heterozygosis InDel and structure variation.
+ .
+ This package contains some example data.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..d6d1f55
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,166 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: pIRS
+Source: ftp://ftp.genomics.org.cn/pub/pIRS/
+Files-Excluded: */gc_coverage_bias
+ */src/pirs/src/pirs
+ */src/pirs/pirs
+ */autom4te.cache
+ */.deps
+ */*.log
+ */stamp-h1
+ */missing
+ */install-sh
+ */depcomp
+ */configure
+ */config.status
+ */config.h*
+ */aclocal.m4
+ */Makefile.in
+ */src/*/Makefile
+ */src/pirs/NEWS
+ */src/pirs/README
+ */src/pirs/src/README
+ */gzstream.*
+
+Files: *
+Copyright: 2011-2013 BGI (http://en.genomics.cn/)
+License: pirs
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ 1. Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ 3. All advertising materials mentioning features or use of this software
+ must display the following acknowledgement:
+ This product includes software developed by Hu Xuesong, Yuan Jianying
+ and Shi Yujian at BGI-Shenzhen and its contributors.
+ 4. Neither the name of the BGI nor the names of its
+ contributors may be used to endorse or promote products derived from
+ this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ POSSIBILITY OF SUCH DAMAGE.
+
+Files: src/pirs/src/MaskQvalsByEamss.*
+Copyright: 2008-2010 Illumina, Inc.
+License: Illumina_non-distributable
+ This software is covered by the "Illumina Genome Analyzer Software
+ License Agreement" and the "Illumina Source Code License Agreement",
+ and certain third party copyright/licenses, and any user of this
+ source file is bound by the terms therein (see accompanying files
+ Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
+ Illumina_Source_Code_License_Agreement.pdf and third party
+ copyright/license notices).
+ .
+ ILLUMINA GENOME ANALYZER SOFTWARE LICENSE AGREEMENT
+ .
+ PLEASE READ THESE TERMS CAREFULLY BEFORE OPENING, INSTALLING, USING, ACCESSING OR MANIPULATING
+ THE SOFTWARE (AS DEFINED BELOW), AS BY SUCH ACTIONS YOU ACKNOWLEDGE THAT YOU HAVE READ THIS
+ AGREEMENT, UNDERSTAND IT AND AGREE TO BE BOUND BY ITS TERMS.
+ .
+ ILLUMINA, INC. (“LICENSOR”) IS WILLING TO LICENSE THE ENCLOSED SOFTWARE (THE “SOFTWARE”) TO YOU ONLY ON
+ THE CONDITION THAT YOU ACCEPT ALL OF THE TERMS IN THIS AGREEMENT. IF YOU DO NOT AGREE TO THESE TERMS,
+ LICENSOR IS UNWILLING TO LICENSE THE SOFTWARE TO YOU, AND YOU SHOULD NOT USE OR INSTALL THE SOFTWARE.
+ .
+ 1. GRANT OF LICENSE. The following grants are subject to the terms and conditions of this Agreement. Licensor
+ grants you a personal, non-exclusive, non-sublicenseable, restricted right to install and use one copy of the Software
+ solely in executable code form and solely in conjunction with the Illumina Genome Analyzer. In the case of
+ Software provided by Licensor in non-compiled form, Licensor grants you a personal, non-exclusive, nonsublicenseable,
+ restricted right to compile, install and use one copy of the Software solely in conjunction with the
+ Illumina Genome Analyzer. You may (i) make one copy of the Software solely for purposes of having a backup
+ copy, provided that you reproduce on that copy all copyright notices and any other confidentiality or proprietary
+ legends that are on the original copy of the Software, or (ii) transfer the Software to a single hard disk provided you
+ keep the original solely as a backup copy. In addition, you are free to modify and/or adapt any Software provided in
+ non-compiled form solely for your own use. You understand that Licensor may update the Software at any time but
+ in doing so incurs no obligation to furnish such updates to you pursuant to this Agreement. Licensor reserves all
+ rights in the Software not expressly granted to you in this Agreement.
+ 2. OWNERSHIP. The Software is and shall remain a proprietary product of Licensor and/or its suppliers. Licensor
+ and/or its suppliers shall retain ownership of all patents, copyrights, trademarks, trade names, trade secrets and other
+ intellectual property rights in the Software. Except as provided in Section 1, you shall have no right, title or interest
+ in or to the Software. The Software is licensed, not sold, to you for use only under the terms of this Agreement.
+ 3. RESTRICTIONS. Except as expressly permitted in Section 1, you may not use, copy, modify, create derivative
+ works of, distribute, sell, assign, pledge, sublicense, lease, loan, rent, timeshare or otherwise transfer the Software,
+ nor permit any other party to do any of the foregoing. You may not remove from the Software, or alter, any of the
+ trademarks, trade names, logos, patent or copyright notices or markings, or add any other notices or markings to the
+ Software. You may not derive or attempt to derive the source code of the Software (other than Software provided
+ by Licensor in non-compiled form) by any means, nor permit any other party to derive or attempt to derive such
+ source code. You may not reverse engineer, decompile, disassemble, or translate the Software (other than Software
+ provided by Licensor in non-compiled form) or any part thereof.
+ 4. TERM. Illumina may terminate this Agreement upon notice to you if you fail to comply with this Agreement, in
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+ this Agreement by discontinuing use of the Software and removing and destroying all copies thereof.
+ 5. WARRANTY DISCLAIMER. THE SOFTWARE IS PROVIDED TO YOU “AS IS” AND LICENSOR AND ITS SUPPLIERS
+ EXPRESSLY DISCLAIM ALL WARRANTIES AND CONDITIONS INCLUDING THE IMPLIED WARRANTIES OR CONDITIONS OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT. NO ORAL OR WRITTEN
+ INFORMATION OR ADVICE GIVEN BY LICENSOR, ITS EMPLOYEES, DISTRIBUTORS, DEALERS, OR AGENTS SHALL
+ INCREASE THE SCOPE OF THE ABOVE WARRANTIES OR CREATE ANY NEW WARRANTIES. Some jurisdictions do not
+ allow the disclaimer of certain implied warranties, so the above disclaimer may not apply to you.
+ 6. LIMITATION OF REMEDIES. REGARDLESS OF WHETHER ANY REMEDY SET FORTH HEREIN FAILS OF ITS ESSENTIAL
+ PURPOSE OR OTHERWISE, IN NO EVENT WILL LICENSOR OR ITS SUPPLIERS BE LIABLE TO YOU OR TO ANY THIRD PARTY
+ FOR ANY LOST PROFITS, LOST DATA, INTERRUPTION OF BUSINESS, OR OTHER SPECIAL, INDIRECT, INCIDENTAL OR
+ CONSEQUENTIAL DAMAGES OF ANY KIND ARISING OUT OF THE USE OR INABILITY TO USE THE SOFTWARE OR ANY DATA
+ SUPPLIED THEREWITH, EVEN IF LICENSOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH LOSS OR DAMAGES AND
+ WHETHER OR NOT SUCH LOSS OR DAMAGES ARE FORESEEABLE. THE CUMULATIVE LIABILITY OF LICENSOR FOR ALL
+ CLAIMS ARISING FROM OR RELATING TO THIS AGREEMENT, INCLUDING WITHOUT LIMITATION, ANY CAUSE OF ACTION
+ SOUNDING IN CONTRACT, TORT, OR STRICT LIABILITY, SHALL NOT EXCEED ONE THOUSAND DOLLARS (USD $1000)..
+ Some jurisdictions do not allow the exclusion or limitation of incidental, consequential, indirect or special damages,
+ so the above limitations may not apply to you.
+ 7. U. S. GOVERNMENT END USERS. If you are a branch agency or instrumentality of the United States
+ Government, the following provision applies. The Software is a “commercial item” as that term is defined at 48
+ C.F.R. 2.101, consisting of “commercial computer software” and “commercial computer software documentation,”
+ as such terms are used in 48 C.F.R. 12.212 or 48 C.F.R. 227.7202 (as applicable). Consistent with 48 C.F.R. 12.212
+ and 48 C.F.R. 227.7202-1 through 227.7202-4, all United States Government end users acquire the Software with
+ only those rights set forth herein.
+ 8. EXPORT LAW. The Software and related technology are subject to U.S. export control laws and may be subject
+ to export or import regulations in other countries. You agree to strictly comply with all such laws and regulations
+ and acknowledge that you have the responsibility to obtain such licenses to export, re-export or import as may be
+ required.
+ 9. GENERAL. This Agreement is governed by the laws of the State of California in the United States of America,
+ without regard to its conflict of laws principles. The federal and state courts of San Diego County in California shall
+ have exclusive jurisdiction of, and venue in, in any dispute arising out of or relating to this Agreement. The United
+ Nations Convention on Contracts for the International Sale of Goods shall not apply to this Agreement. If any
+ provision of this Agreement is held to be unenforceable, that provision will be removed and the remaining
+ provisions will remain in full force. This Agreement is the complete and exclusive statement of the agreement
+ between us which supersedes any proposal or prior agreement, oral or written, and any other communications
+ between us in relation to the subject matter of this Agreement. The relationship between you and us is that of
+ licensee/licensor. Neither party will represent that it has any authority to assume or create any obligation, express or
+ implied, on behalf of the other party, nor to represent the other party as agent, employee, franchisee, or in any other
+ capacity.
+ .
+ If you have any questions regarding this Agreement or the Software, please contact TechSupport at illumina.com.
+ THE SOFTWARE IS PROTECTED BY UNITED STATES COPYRIGHT LAW AND INTERNATIONAL TREATY.
+ UNAUTHORIZED REPRODUCTION OR DISTRIBUTION IS SUBJECT TO CIVIL AND CRIMINAL PENALTIES.
+
+Files: src/stator/gcContCvgBias/*
+Copyright: 2012-2013 Xuesong Hu <galaxy001 at gmail.com>
+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 the full text of the GNU General Public
+ License version 2 at /usr/share/common-licenses/GPL-2.
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..14d3581
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+use_debian_packaged_libgzstream.patch
diff --git a/debian/patches/use_debian_packaged_libgzstream.patch b/debian/patches/use_debian_packaged_libgzstream.patch
new file mode 100644
index 0000000..7c9b152
--- /dev/null
+++ b/debian/patches/use_debian_packaged_libgzstream.patch
@@ -0,0 +1,69 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 02 Aug 2016 12:12:20 +0200
+Description: Replace Files-Excluded code copy of gzstream by Debian packaged version
+
+--- a/src/stator/gcContCvgBias/Makefile.am
++++ b/src/stator/gcContCvgBias/Makefile.am
+@@ -2,5 +2,5 @@ AUTOMAKE_OPTIONS=gnu
+ SUBDIRS = src
+ bindir=$(prefix)/
+ bin_PROGRAMS=gc_coverage_bias
+-gc_coverage_bias_SOURCES=$(SUBDIRS)/main.cpp $(SUBDIRS)/self_util.cpp $(SUBDIRS)/stat_soap_coverage.cpp $(SUBDIRS)/gzstream.cpp
++gc_coverage_bias_SOURCES=$(SUBDIRS)/main.cpp $(SUBDIRS)/self_util.cpp $(SUBDIRS)/stat_soap_coverage.cpp
+
+--- a/src/stator/gcContCvgBias/configure.ac
++++ b/src/stator/gcContCvgBias/configure.ac
+@@ -4,7 +4,7 @@
+ AC_PREREQ(2.59)
+ AC_INIT(gc_coverage_bias)
+ AM_INIT_AUTOMAKE(gc_coverage_bias,1.0)
+-AC_CONFIG_SRCDIR([src/gzstream.cpp])
++AC_CONFIG_SRCDIR([src/main.cpp])
+ AC_CONFIG_HEADER([config.h])
+
+ # Checks for programs.
+@@ -15,6 +15,8 @@ AC_PROG_CC
+ # FIXME: Replace `main' with a function in `-lz':
+ AC_CHECK_LIB([z], [main])
+
++AC_CHECK_LIB([gzstream], [main])
++
+ # Checks for header files.
+ AC_HEADER_STDC
+ AC_CHECK_HEADERS([stdint.h string.h])
+--- a/src/pirs/Makefile.am
++++ b/src/pirs/Makefile.am
+@@ -9,4 +9,4 @@ profile3_DATA=$(SUBDIRS)/Profiles/GC-dep
+ AUTOMAKE_OPTIONS=gnu
+ bindir=$(prefix)/
+ bin_PROGRAMS=pirs
+-pirs_SOURCES=$(SUBDIRS)/main.cpp $(SUBDIRS)/simulate_Illumina_reads.cpp $(SUBDIRS)/simulate_diploid_genome.cpp $(SUBDIRS)/simulate.cpp $(SUBDIRS)/load_file.cpp $(SUBDIRS)/MaskQvalsByEamss.cpp $(SUBDIRS)/gzstream.cpp
++pirs_SOURCES=$(SUBDIRS)/main.cpp $(SUBDIRS)/simulate_Illumina_reads.cpp $(SUBDIRS)/simulate_diploid_genome.cpp $(SUBDIRS)/simulate.cpp $(SUBDIRS)/load_file.cpp $(SUBDIRS)/MaskQvalsByEamss.cpp
+--- a/src/pirs/configure.ac
++++ b/src/pirs/configure.ac
+@@ -15,6 +15,8 @@ AC_PROG_CC
+ # FIXME: Replace `main' with a function in `-lz':
+ AC_CHECK_LIB([z], [main])
+
++AC_CHECK_LIB([gzstream], [main])
++
+ # Checks for header files.
+ AC_HEADER_STDC
+ AC_CHECK_HEADERS([stdlib.h string.h])
+--- a/src/stator/gcContCvgBias/src/Makefile.am
++++ b/src/stator/gcContCvgBias/src/Makefile.am
+@@ -1,5 +1,5 @@
+ AUTOMAKE_OPTIONS=gnu
+ bindir=$(prefix)/
+ bin_PROGRAMS=gc_coverage_bias
+-gc_coverage_bias_SOURCES=main.cpp self_util.cpp stat_soap_coverage.cpp gzstream.cpp
++gc_coverage_bias_SOURCES=main.cpp self_util.cpp stat_soap_coverage.cpp
+
+--- a/src/pirs/src/Makefile.am
++++ b/src/pirs/src/Makefile.am
+@@ -8,4 +8,4 @@ profile3_DATA=Profiles/GC-depth_Profiles
+ AUTOMAKE_OPTIONS=gnu
+ bindir=$(prefix)/
+ bin_PROGRAMS=pirs
+-pirs_SOURCES=main.cpp simulate_Illumina_reads.cpp simulate_diploid_genome.cpp simulate.cpp load_file.cpp MaskQvalsByEamss.cpp gzstream.cpp
++pirs_SOURCES=main.cpp simulate_Illumina_reads.cpp simulate_diploid_genome.cpp simulate.cpp load_file.cpp MaskQvalsByEamss.cpp
diff --git a/debian/pirs-examples.install b/debian/pirs-examples.install
new file mode 100644
index 0000000..0a82ff5
--- /dev/null
+++ b/debian/pirs-examples.install
@@ -0,0 +1,2 @@
+src/pirs/src/test/*.fa usr/share/doc/pirs/examples/pirs
+src/stator/gcContCvgBias/src/test/gc* usr/share/doc/pirs/examples/gcContCvgBias
diff --git a/debian/pirs-profiles.install b/debian/pirs-profiles.install
new file mode 100644
index 0000000..18d028a
--- /dev/null
+++ b/debian/pirs-profiles.install
@@ -0,0 +1 @@
+src/pirs/src/Profiles usr/share/pirs
diff --git a/debian/pirs-profiles.lintian-overrides b/debian/pirs-profiles.lintian-overrides
new file mode 100644
index 0000000..576d468
--- /dev/null
+++ b/debian/pirs-profiles.lintian-overrides
@@ -0,0 +1,2 @@
+# The gz files are verbose copies from upstream tarball
+pirs-profiles: package-contains-timestamped-gzip usr/share/pirs/Profiles/Base-Calling_Profiles/*.matrix.gz
diff --git a/debian/pirs.docs b/debian/pirs.docs
new file mode 100644
index 0000000..e845566
--- /dev/null
+++ b/debian/pirs.docs
@@ -0,0 +1 @@
+README
diff --git a/debian/pirs.install b/debian/pirs.install
new file mode 100644
index 0000000..3525799
--- /dev/null
+++ b/debian/pirs.install
@@ -0,0 +1,2 @@
+src/pirs/src/pirs usr/bin
+src/stator/gcContCvgBias/src/gc_coverage_bias usr/bin
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..17485c2
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,68 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+PERLDIR := debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)
+
+SRCDIRS=src/pirs src/stator/gcContCvgBias
+
+%:
+ dh $@ --with autoreconf --sourcedirectory=src/pirs
+
+override_dh_auto_clean:
+ for srcdir in $(SRCDIRS) ; do \
+ dh_auto_clean --sourcedirectory=$${srcdir} ; \
+ done
+
+override_dh_autoreconf:
+ # does not work - no idea why
+ # dh_autoreconf --sourcedirectory=src/pirs
+ #
+ # Hmmm, duplicated NEWS and README were removed via Files-Excluded - this is firing back now ...
+ ln -s $(CURDIR)/NEWS src/pirs
+ ln -s $(CURDIR)/README src/pirs
+ for srcdir in $(SRCDIRS) ; do \
+ cd $${srcdir} && \
+ mv INSTALL INSTALL.save && \
+ autoreconf --install && \
+ mv INSTALL.save INSTALL && \
+ cd $(CURDIR) ; \
+ done
+ rm src/pirs/NEWS src/pirs/README
+
+override_dh_auto_configure:
+ for srcdir in $(SRCDIRS) ; do \
+ dh_auto_configure --sourcedirectory=$${srcdir} ; \
+ done
+
+override_dh_auto_build:
+ for srcdir in $(SRCDIRS) ; do \
+ dh_auto_build --sourcedirectory=$${srcdir} ; \
+ done
+
+override_dh_auto_install:
+ dh_auto_install --sourcedirectory=src/stator/gcContCvgBias
+
+override_dh_install:
+ dh_install
+ mkdir -p $(PERLDIR)
+ find src -name "*.pl" -exec cp -a \{\} $(PERLDIR) \;
+ rm -f $(PERLDIR)/autobam.pl
+ sed -i 's:#!/bin/env:#!/usr/bin/env:' $(PERLDIR)/*.pl
+
+override_dh_link:
+ dh_link
+ for pl in $(PERLDIR)/*.pl ; do \
+ plname=`basename $${pl}` ; \
+ ln -s ../lib/$(DEBPKGNAME)/$${plname} debian/$(DEBPKGNAME)/usr/bin/`basename $${plname} .pl` ; \
+ done
+
+override_dh_installchangelogs:
+ dh_installchangelogs NEWS
+
+override_dh_installdocs:
+ dh_installdocs
+ cp -a src/stator/readme.txt debian/$(DEBPKGNAME)/usr/share/doc/$(DEBPKGNAME)/strator_readme.txt
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..3473d90
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Xuesong Hu and Jianying Yuan and Yujian Shi and Jianliang Lu and Binghang Liu and Zhenyu Li and Yanxiang Chen and Desheng Mu and Hao Zhang and Nan Li and Zhen Yue and Fan Bai and Heng Li and Wei Fan
+ Title: "pIRS: Profile-based Illumina pair-end reads simulator"
+ Journal: Bioinformatics
+ Year: 2012
+ Volume: 28
+ Number: 11
+ Pages: 1533-5
+ DOI: 10.1093/bioinformatics/bts187
+ PMID: 22508794
+ URL: http://bioinformatics.oxfordjournals.org/content/28/11/1533
+ eprint: http://bioinformatics.oxfordjournals.org/content/28/11/1533.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..2ae6c0b
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="uversionmangle=s/b/~b/;s/(\d)(\d+)/$1.$2/,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ ftp://ftp.genomics.org.cn/pub/pIRS/pIRS_(\d+)\.tgz
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