[med-svn] [hilive] 02/02: Inject initial packaging
Andreas Tille
tille at debian.org
Fri Jul 29 12:19:24 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository hilive.
commit 4f3bc754347c30cb5c4571a3e8b044abf421d610
Author: Andreas Tille <tille at debian.org>
Date: Fri Jul 29 14:17:48 2016 +0200
Inject initial packaging
---
debian/changelog | 5 ++
debian/compat | 1 +
debian/control | 27 ++++++++++
debian/copyright | 22 ++++++++
debian/createmanpages | 28 ++++++++++
debian/get-orig-source | 25 +++++++++
debian/hilive-build.1 | 34 +++++++++++++
debian/hilive.1 | 96 +++++++++++++++++++++++++++++++++++
debian/install | 4 ++
debian/manpages | 1 +
debian/patches/do_not_set_rpath.patch | 17 +++++++
debian/patches/fix_cmath.patch | 13 +++++
debian/patches/series | 2 +
debian/rules | 14 +++++
debian/source/format | 1 +
debian/watch | 4 ++
16 files changed, 294 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..94827ca
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+hilive (0.0+20150926-1) 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/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..27ee663
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,27 @@
+Source: hilive
+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,
+ libboost-system-dev,
+ libboost-filesystem-dev,
+ libboost-program-options-dev,
+ zlib1g-dev,
+ liblz4-dev,
+ chrpath
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/hilive.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/hilive.git
+Homepage: https://sourceforge.net/projects/hilive/
+
+Package: hilive
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: realtime alignment of Illumina reads
+ HiLive is a read mapping tool that maps Illumina HiSeq (or comparable)
+ reads to a reference genome right in the moment when they are produced.
+ This means, read mapping is finished as soon as the sequencer is
+ finished generating the data.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..da21dde
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,22 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: HiLive
+Source: https://sourceforge.net/projects/hilive/
+
+Files: *
+Copyright: 2015 Martin S. Lindner <marzin at mail-lindner.de>
+License: BSD-3-clause
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: BSD-3-clause
+
+License: BSD-3-clause
+ 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. Neither the name of the copyright holder 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 HOLDER 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 PRO [...]
\ No newline at end of file
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..8d7c70a
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,28 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=hilive-build
+help2man --no-info --no-discard-stderr \
+ --name='Index creation tool for HiLive - Realtime Alignment of Illumina Reads' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=hilive
+help2man --no-info --no-discard-stderr \
+ --name='Realtime Alignment of Illumina Reads' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..1274061
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,25 @@
+#!/bin/sh -e
+
+COMPRESS=xz
+
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+MVERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/^\([0-9\.]\+\)[+~][-0-9]\+$/\1/'`
+
+mkdir -p ../tarballs
+cd ../tarballs
+# need to clean up the tarballs dir first because upstream tarball might
+# contain a directory with unpredictable name
+rm -rf *
+set -x
+git clone --quiet http://git.code.sf.net/p/hilive/code $NAME
+cd $NAME
+VERSION=${MVERSION}+`date -d @$(git show --format="%at" | head -n1) +%Y%m%d`
+# for esthetical reasons set file timestamps (if git-restore-mtime is installed)
+git restore-mtime || true
+cd ..
+TARDIR=${NAME}-${VERSION}
+mv ${NAME} ${TARDIR}
+rm -rf ${TARDIR}/.git*
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}
diff --git a/debian/hilive-build.1 b/debian/hilive-build.1
new file mode 100644
index 0000000..f3061a0
--- /dev/null
+++ b/debian/hilive-build.1
@@ -0,0 +1,34 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH HILIVE-BUILD "1" "July 2016" "hilive-build 0.0+20150926" "User Commands"
+.SH NAME
+hilive-build \- Index creation tool for HiLive - Realtime Alignment of Illumina Reads
+.SH SYNOPSIS
+.B hilive-build
+[\fI\,options\/\fR] \fI\,INPUT\/\fR
+.SH DESCRIPTION
+HiLive index builder v0.1
+Index creation tool for HiLive \- Realtime Alignment of Illumina Reads
+Copyright \(co 2015, Martin S. Lindner
+HiLive is open\-source software. Check with \fB\-\-license\fR for details.
+.PP
+Fixed k\-mer size: 15
+.TP
+INPUT
+Reference genomes in (multi\-) FASTA format
+.SS "General:"
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+Print this help message and exit
+.TP
+\fB\-\-license\fR
+Print licensing information and exit
+.SH OPTIONS
+.TP
+\fB\-o\fR [ \fB\-\-outfile\fR ] arg
+Set output file name [Default: INPUT.kix]
+.TP
+\fB\-t\fR [ \fB\-\-trim\fR ] arg
+Ignore k\-mers with more than t occurrences. [Default:
+no limit]
+.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/hilive.1 b/debian/hilive.1
new file mode 100644
index 0000000..bb9b13a
--- /dev/null
+++ b/debian/hilive.1
@@ -0,0 +1,96 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH HILIVE "1" "July 2016" "hilive 0.0+20150926" "User Commands"
+.SH NAME
+hilive \- Realtime Alignment of Illumina Reads
+.SH SYNOPSIS
+.B hilive
+[\fI\,options\/\fR] \fI\,BC_DIR INDEX CYCLES\/\fR
+.SH DESCRIPTION
+HiLive v0.1 \- Realtime Alignment of Illumina Reads
+Copyright \(co 2015, Martin S. Lindner
+HiLive is open\-source software. Check with \fB\-\-license\fR for details.
+.PP
+Fixed k\-mer size: 15
+.TP
+BC_DIR
+Illumina BaseCalls directory of the sequencing run to analyze
+.TP
+INDEX
+Path to k\-mer index file (*.kix)
+.TP
+CYCLES
+Total number of cycles for read 1
+.SS "General:"
+.TP
+\fB\-h\fR [ \fB\-\-help\fR ]
+Print this help message and exit
+.TP
+\fB\-\-license\fR
+Print licensing information and exit
+.SS "IO settings:"
+.TP
+\fB\-\-temp\fR arg
+Temporary directory for the alignment files
+[Default: use BaseCalls directory]
+.TP
+\fB\-S\fR [ \fB\-\-sam\fR ] arg
+Create SAM files for each tile. [Default: no
+SAM files]
+.TP
+\fB\-k\fR [ \fB\-\-keep\-files\fR ]
+Keep intermediate alignment files [Default:
+false]
+.TP
+\fB\-l\fR [ \fB\-\-lanes\fR ] arg
+Select lane [Default: all lanes]
+.TP
+\fB\-t\fR [ \fB\-\-tiles\fR ] arg
+Select tile numbers [Default: all tiles]
+.SS "Alignment settings:"
+.TP
+\fB\-e\fR [ \fB\-\-min\-errors\fR ] arg (=2)
+Number of errors tolerated in read alignment
+.TP
+\fB\-H\fR [ \fB\-\-best\-hit\fR ]
+Report only the best alignmnet(s) for each
+read
+.TP
+\fB\-N\fR [ \fB\-\-best\-n\fR ] arg (=2)
+Report the N best alignmnets for each read
+.TP
+\fB\-\-disable\-ohw\-filter\fR
+Disable the One\-Hit Wonder filter
+.TP
+\fB\-\-start\-ohw\fR arg (=20)
+First cycle to apply One\-Hit Wonder filter
+.TP
+\fB\-w\fR [ \fB\-\-window\fR ] arg (=5)
+Set the window size to search for alignment
+continuation, i.e. maximum insertion/deletion
+size
+.TP
+\fB\-\-min\-quality\fR arg (=1)
+Minimum allowed basecall quality
+.SS "Technical settings:"
+.TP
+\fB\-\-block\-size\fR arg
+Block size for the alignment input/output
+stream in Bytes. Use \fB\-K\fR or \fB\-M\fR to specify in
+Kilobytes or Megabytes
+.TP
+\fB\-K\fR
+Interpret the block\-size argument as Kilobytes
+instead of Bytes
+.TP
+\fB\-M\fR
+Interpret the block\-size argument as Megabytes
+instead of Bytes
+.TP
+\fB\-c\fR [ \fB\-\-compression\fR ] arg (=2)
+Compress alignment files. 0: no compression
+(default) 1: Deflate (smaller) 2: LZ4 (faster)
+.TP
+\fB\-n\fR [ \fB\-\-num\-threads\fR ] arg (=1)
+Number of threads to spawn
+.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/install b/debian/install
new file mode 100644
index 0000000..0d2bf24
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,4 @@
+obj-*/hilive usr/bin
+obj-*/hilive-build usr/bin
+
+
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/patches/do_not_set_rpath.patch b/debian/patches/do_not_set_rpath.patch
new file mode 100644
index 0000000..60c7671
--- /dev/null
+++ b/debian/patches/do_not_set_rpath.patch
@@ -0,0 +1,17 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 28 Jul 2016 15:13:14 +0200
+Description: Do not set rpath
+ Unfortunately this does not work and chrpath needs to be used.
+ .
+ Any hint to do this properly is welcome.
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -35,6 +35,7 @@ foreach (lib ${LIBS})
+ list(APPEND LIB_FILES "lib/${lib}.cpp")
+ endforeach()
+ add_library(hilivelib ${LIB_FILES})
++set_target_properties(hilivelib PROPERTIES SKIP_BUILD_RPATH TRUE)
+
+ set(Boost_USE_STATIC_LIBS ON)
+ set(Boost_USE_MULTITHREADED ON)
diff --git a/debian/patches/fix_cmath.patch b/debian/patches/fix_cmath.patch
new file mode 100644
index 0000000..b36015f
--- /dev/null
+++ b/debian/patches/fix_cmath.patch
@@ -0,0 +1,13 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 28 Jul 2016 15:13:14 +0200
+Description: Add missing header file
+
+--- a/lib/alnread.cpp
++++ b/lib/alnread.cpp
+@@ -1,5 +1,6 @@
+ #include <time.h>
+ #include <chrono>
++#include <cmath>
+
+ #include "alnread.h"
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..5d11aea
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+fix_cmath.patch
+do_not_set_rpath.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..518d1ba
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,14 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
+
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+
+%:
+ dh $@
+
+override_dh_install:
+ chrpath --delete obj-$(DEB_BUILD_GNU_TYPE)/hilive*
+ dh_install
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/watch b/debian/watch
new file mode 100644
index 0000000..1b4b054
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ https://github.com/biobenkj/SPARTA_Linux/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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