[med-svn] [adapterremoval] 02/02: Add initial packaging
Andreas Tille
tille at debian.org
Thu Jul 28 14:23:29 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository adapterremoval.
commit d17f764033832c5547687eb1df151bb3978b3d26
Author: Andreas Tille <tille at debian.org>
Date: Thu Jul 28 16:22:10 2016 +0200
Add initial packaging
---
debian/README.test | 9 +++++++
debian/adapterremoval-examples.install | 1 +
debian/adapterremoval.docs | 3 +++
debian/adapterremoval.install | 1 +
debian/adapterremoval.manpages | 1 +
debian/changelog | 5 ++++
debian/clean | 1 +
debian/compat | 1 +
debian/control | 43 ++++++++++++++++++++++++++++++++++
debian/copyright | 25 ++++++++++++++++++++
debian/patches/hardening.patch | 24 +++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 25 ++++++++++++++++++++
debian/source/format | 1 +
debian/tests/control | 3 +++
debian/tests/run-unit-test | 20 ++++++++++++++++
debian/upstream/metadata | 11 +++++++++
debian/watch | 3 +++
18 files changed, 178 insertions(+)
diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..c2148dd
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,9 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+To run the unit tests provided by the package can run
+
+ sh run-unit-test
+
+in this directory. To run the tests you need to install
+the adapterremoval-examples package.
diff --git a/debian/adapterremoval-examples.install b/debian/adapterremoval-examples.install
new file mode 100644
index 0000000..b344a40
--- /dev/null
+++ b/debian/adapterremoval-examples.install
@@ -0,0 +1 @@
+examples usr/share/doc/adapterremoval
diff --git a/debian/adapterremoval.docs b/debian/adapterremoval.docs
new file mode 100644
index 0000000..0c8da32
--- /dev/null
+++ b/debian/adapterremoval.docs
@@ -0,0 +1,3 @@
+README.html
+debian/README.test
+debian/tests/run-unit-test
diff --git a/debian/adapterremoval.install b/debian/adapterremoval.install
new file mode 100644
index 0000000..56fcd58
--- /dev/null
+++ b/debian/adapterremoval.install
@@ -0,0 +1 @@
+build/AdapterRemoval usr/bin
diff --git a/debian/adapterremoval.manpages b/debian/adapterremoval.manpages
new file mode 100644
index 0000000..9ac5e51
--- /dev/null
+++ b/debian/adapterremoval.manpages
@@ -0,0 +1 @@
+build/AdapterRemoval.1
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..7072479
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+adapterremoval (2.1.7-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Thu, 28 Jul 2016 15:13:14 +0200
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..daa30a3
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+README.html
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..089e231
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,43 @@
+Source: adapterremoval
+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),
+ zlib1g-dev,
+ libbz2-dev,
+ libgtest-dev,
+ python-markdown
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/adapterremoval.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/adapterremoval.git
+Homepage: https://github.com/MikkelSchubert/adapterremoval
+
+Package: adapterremoval
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: rapid adapter trimming, identification, and read merging of gene sequences
+ This program searches for and removes remnant adapter sequences from High-
+ Throughput Sequencing (HTS) data and (optionally) trims low quality
+ bases from the 3' end of reads following adapter removal. AdapterRemoval
+ can analyze both single end and paired end data, and can be used to
+ merge overlapping paired-ended reads into (longer) consensus sequences.
+ Additionally, the AdapterRemoval may be used to recover a consensus
+ adapter sequence for paired-ended data, for which this information is
+ not available.
+
+Package: adapterremoval-examples
+Architecture: all
+Depends: ${misc:Depends}
+Description: rapid adapter trimming, identification, and read merging (example data)
+ This program searches for and removes remnant adapter sequences from High-
+ Throughput Sequencing (HTS) data and (optionally) trims low quality
+ bases from the 3' end of reads following adapter removal. AdapterRemoval
+ can analyze both single end and paired end data, and can be used to
+ merge overlapping paired-ended reads into (longer) consensus sequences.
+ Additionally, the AdapterRemoval may be used to recover a consensus
+ adapter sequence for paired-ended data, for which this information is
+ not available.
+ .
+ This package provides the example data.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..72ad7e7
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,25 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: AdapterRemoval
+Source: https://github.com/MikkelSchubert/adapterremoval/releases
+
+Files: *
+Copyright: 2012-2016 Mikkel Schubert, Stinus Lindgreen and Ludovic Orlando
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: GPL-3+
+
+License: GPL-3+
+ 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 3 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 full copy of the GNU General Public
+ License version 3 at /usr/share/common-licenses/GPL-3.
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
new file mode 100644
index 0000000..40301d6
--- /dev/null
+++ b/debian/patches/hardening.patch
@@ -0,0 +1,24 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 28 Jul 2016 15:13:14 +0200
+Description: Propagate hardening options
+
+--- a/Makefile
++++ b/Makefile
+@@ -6,7 +6,7 @@
+ PREFIX := /usr/local
+
+ # Default compilation flags
+-CXXFLAGS := -O3 -ansi -pedantic -Wall -Wextra
++CXXFLAGS += -O3 -ansi -pedantic -Wall -Wextra
+ CXXFLAGS := ${CXXFLAGS} -Wcast-align -Wcast-qual -Wctor-dtor-privacy \
+ -Wdisabled-optimization -Wformat=2 -Winit-self -Wold-style-cast \
+ -Woverloaded-virtual -Wredundant-decls -Wsign-promo -Wstrict-overflow=5 \
+@@ -146,7 +146,7 @@ $(BDIR)/%.o: src/%.cc
+ # Executable
+ build/$(PROG): $(OBJS)
+ @echo $(COLOR_GREEN)"Linking executable '$@'"$(COLOR_END)
+- $(QUIET) $(CXX) $(CXXFLAGS) $^ ${LIBRARIES} -o $@
++ $(QUIET) $(CXX) $(CXXFLAGS) $^ ${LIBRARIES} -o $@ ${LDFLAGS}
+
+ # Static library
+ build/$(LIBNAME).a: $(LIBOBJS)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..814900f
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+hardening.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..285a16b
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,25 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ dh_auto_build
+ markdown_py -f README.html README.md
+
+override_dh_auto_test:
+ # dh_auto_test
+ echo "*********** Needs adapting to libgtest-dev. ***************"
+
+override_dh_auto_install:
+ make PREFIX=$(CURDIR)/debian/$(DEBPKGNAME)/usr
+ # Hmmm, this does nothing ...
+
+override_dh_installchangelogs:
+ dh_installchangelogs CHANGES.md
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..d2aa55a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..7d65af4
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,20 @@
+#!/bin/sh -e
+
+pkg=adapterremoval
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/examples/* .
+find . -name "*.gz" -exec gunzip \{\} \;
+
+# examples from README.html
+AdapterRemoval --file1 reads_1.fq --basename output_single --trimns --trimqualities --gzip
+AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_paired --trimns --trimqualities --collapse
+AdapterRemoval --interleaved --file1 interleaved.fq --basename output_interleaved
+AdapterRemoval --qualitybase 64 --file1 reads_q64.fq --basename phred_64_encoded
+AdapterRemoval --qualitybase 64 --qualitybase-output 33 --file1 reads_q64.fq --basename phred_33_encoded
+AdapterRemoval --qualitymax 50 --file1 reads_1.fq --file2 reads_2.fq --collapsed --basename collapsed_q50
+AdapterRemoval --file1 reads_1.fq --file2 reads_2.fq --basename output_multi --trimns --trimqualities --collapse --adapter-list adapters.txt
+AdapterRemoval --identify-adapters --file1 reads_1.fq --file2 reads_2.fq
+AdapterRemoval --file1 demux_1.fq --file2 demux_2.fq --basename output_dumux --barcode-list barcodes.txt
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..c9ed98b
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Mikkel Schubert and Stinus Lindgreen and Ludovic Orlando
+ Title: "AdapterRemoval v2: rapid adapter trimming, identification, and read merging"
+ Journal: BMC Research Notes
+ Year: 2016
+ Volume: 9
+ Pages: 88
+ DOI: 10.1186/s13104-016-1900-2
+ PMID: 26868221
+ URL: http://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-016-1900-2
+ eprint: http://bmcresnotes.biomedcentral.com/track/pdf/10.1186/s13104-016-1900-2
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..23f7a9f
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/MikkelSchubert/adapterremoval/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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