[med-svn] [quorum] 02/02: initial packaging
Andreas Tille
tille at debian.org
Wed May 17 13:51:12 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository quorum.
commit fa9d89c3681895440ba7589ebbeb095e6ac74505
Author: Andreas Tille <tille at debian.org>
Date: Wed May 17 15:50:42 2017 +0200
initial packaging
---
debian/changelog | 5 ++
debian/clean | 5 ++
debian/compat | 1 +
debian/control | 30 ++++++++++++
debian/copyright | 66 ++++++++++++++++++++++++++
debian/createmanpages | 46 ++++++++++++++++++
debian/manpages | 1 +
debian/mans/merge_mate_pairs.1 | 20 ++++++++
debian/mans/quorum.1 | 74 +++++++++++++++++++++++++++++
debian/mans/quorum_create_database.1 | 47 ++++++++++++++++++
debian/mans/quorum_error_correct_reads.1 | 81 ++++++++++++++++++++++++++++++++
debian/mans/split_mate_pairs.1 | 20 ++++++++
debian/rules | 15 ++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++++
debian/watch | 3 ++
16 files changed, 427 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..6f482ac
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+quorum (1.1.1-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 16 May 2017 14:25:24 +0200
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..7581a86
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1,5 @@
+config.log
+src/create_database_cmdline.hpp
+src/error_correct_reads_cmdline.hpp
+src/merge_mate_pairs_cmdline.hpp
+src/split_mate_pairs_cmdline.hpp
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..b6abf72
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,30 @@
+Source: quorum
+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 (>= 10),
+ libjellyfish-2.0-dev (>= 2.2.6-1~),
+ jellyfish (>= 2.2.6-1~),
+ yaggo,
+ pkg-config
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/quorum.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/quorum.git
+Homepage: https://github.com/gmarcais/Quorum
+
+Package: quorum
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: QUality Optimized Reads of genomic sequences
+ QuorUM enables to obtain trimmed and error-corrected reads that result
+ in assemblies with longer contigs and fewer errors. QuorUM provides best
+ performance compared to other published error correctors in several
+ metrics. QuorUM is efficiently implemented making use of current multi-
+ core computing architectures and it is suitable for large data sets (1
+ billion bases checked and corrected per day per core). The third-party
+ assembler (SOAPdenovo) benefits significantly from using QuorUM error-
+ corrected reads. QuorUM error corrected reads result in a factor of 1.1
+ to 4 improvement in N50 contig size compared to using the original reads
+ with SOAPdenovo for the data sets investigated.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..776a179
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,66 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Quorum
+Upstream-Contact: Guillaume Marçais <gmarcais at umd.edu>
+ Aleksey Zimin <alekseyz at ipst.umd.edu>
+Source: https://github.com/gmarcais/Quorum/releases
+
+Files: *
+Copyright: 2012-2016 Guillaume Marçais <gmarcais at umd.edu>,
+ Aleksey Zimin <alekseyz at ipst.umd.edu>,
+ Copyright: 2012, Genome group at University of Maryland
+License: GPL-3+
+
+Files: unit_tests/gtest
+Copyright: 2005, 2006, 2008 Zhanyong Wan <wan at google.com> Google Inc.
+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:
+ .
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * 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.
+ * Neither the name of Google Inc. 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: include/jflib/multiplexed_io.hpp
+Copyright: 2012, Genome group at University of Maryland.
+License: GPL-3+
+
+Files: include/jflib/*
+Copyright: 2012, Genome group at University of Maryland.
+License: GPL-3+
+
+Files: debian/*
+Copyright: 2017 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 copy of the full text of the GNU General
+ Public License version 3 at /usr/share/common-licenses/GPL-3.
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..ca00a80
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,46 @@
+#!/bin/sh
+MANDIR=debian/mans
+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 $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=merge_mate_pairs
+help2man --no-info --no-discard-stderr \
+ --name='interleave sequences from even and odd files' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=quorum
+help2man --no-info --no-discard-stderr \
+ --name='run quorum error corrector on fastq file' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=quorum_create_database
+help2man --no-info --no-discard-stderr \
+ --name='create database of k-mers for quorum error corrector' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=quorum_error_correct_reads
+help2man --no-info --no-discard-stderr \
+ --name='error correct reads from a fastq file based on the k-mer frequencies' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=split_mate_pairs
+help2man --no-info --no-discard-stderr \
+ --name='split fasta file in two' \
+ --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/manpages b/debian/manpages
new file mode 100644
index 0000000..63ab24a
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*
diff --git a/debian/mans/merge_mate_pairs.1 b/debian/mans/merge_mate_pairs.1
new file mode 100644
index 0000000..6dc2556
--- /dev/null
+++ b/debian/mans/merge_mate_pairs.1
@@ -0,0 +1,20 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH MERGE_MATE_PAIRS "1" "May 2017" "merge_mate_pairs 1.1.1" "User Commands"
+.SH NAME
+merge_mate_pairs \- interleave sequences from even and odd files
+.SH DESCRIPTION
+Merge input files
+.PP
+Take an even number of files and interleave sequences from even and odd files.
+.SS "Options (default value in (), *required):"
+.TP
+\fB\-U\fR, \fB\-\-usage\fR
+Usage
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+This message
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+Version
+.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/quorum.1 b/debian/mans/quorum.1
new file mode 100644
index 0000000..55bc8e7
--- /dev/null
+++ b/debian/mans/quorum.1
@@ -0,0 +1,74 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH QUORUM "1" "May 2017" "quorum 1.1.1" "User Commands"
+.SH NAME
+quorum \- run quorum error corrector on fastq file
+.SH DESCRIPTION
+\fI\,/usr/bin/quorum\/\fP [options] .fastq [.fastq]+
+.PP
+Run the quorum error corrector on the given fastq file. If the \fB\-\-paired\-files\fR
+switch is given, quorum expect an even number of files on the command line,
+each pair files containing pair end reads. The output will be two files
+(<prefix>_1.fa and <prefix>_2.fa) containing error corrected pair end reads.
+.SH OPTIONS
+.TP
+\fB\-s\fR, \fB\-\-size\fR
+Mer database size (default 200M)
+.TP
+\fB\-t\fR, \fB\-\-threads\fR
+Number of threads (default number of cpus)
+.TP
+\fB\-p\fR, \fB\-\-prefix\fR
+Output prefix (default quorum_corrected)
+.TP
+\fB\-k\fR, \fB\-\-kmer\-len\fR
+Kmer length (default 24)
+.TP
+\fB\-q\fR, \fB\-\-min\-q\-char\fR
+Minimum quality char. Usually 33 or 64 (autodetect)
+.TP
+\fB\-m\fR, \fB\-\-min\-quality\fR
+Minimum above \fB\-q\fR for high quality base (5)
+.TP
+\fB\-w\fR, \fB\-\-window\fR
+Window size for trimming
+.TP
+\fB\-e\fR, \fB\-\-error\fR
+Maximum number of errors in a window
+.TP
+\fB\-\-min\-count\fR
+Minimum count for a k\-mer to be good
+.TP
+\fB\-\-skip\fR
+Number of bases to skip to find anchor kmer
+.TP
+\fB\-\-anchor\fR
+Numer of good kmer in a row for anchor
+.TP
+\fB\-\-anchor\-count\fR
+Minimum count for an anchor kmer
+.TP
+\fB\-\-contaminant\fR
+Contaminant sequences
+.TP
+\fB\-\-trim\-contaminant\fR
+Trim sequences with contaminant mers
+.TP
+\fB\-d\fR, \fB\-\-no\-discard\fR
+Do not discard reads, output a single N (false)
+.TP
+\fB\-P\fR, \fB\-\-paired\-files\fR
+Preserve mate pairs in two files
+.TP
+\fB\-\-homo\-trim\fR
+Trim homo\-polymer on 3' end
+.TP
+\fB\-\-debug\fR
+Display debugging information
+.TP
+\fB\-\-version\fR
+Display version
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+This 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/quorum_create_database.1 b/debian/mans/quorum_create_database.1
new file mode 100644
index 0000000..0a747d1
--- /dev/null
+++ b/debian/mans/quorum_create_database.1
@@ -0,0 +1,47 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH QUORUM_CREATE_DATABASE "1" "May 2017" "quorum_create_database 1.1.1" "User Commands"
+.SH NAME
+quorum_create_database \- create database of k-mers for quorum error corrector
+.SH SYNOPSIS
+.B create_database_cmdline
+[\fI\,options\/\fR] \fI\,reads:path+\/\fR
+.SH DESCRIPTION
+Create database of k\-mers for quorum error corrector
+.PP
+Create k\-mer database for quorum_error_correct
+.SS "Options (default value in (), *required):"
+.TP
+\fB\-s\fR, \fB\-\-size\fR=\fI\,uint64\/\fR
+*Initial hash size
+.TP
+\fB\-m\fR, \fB\-\-mer\fR=\fI\,uint32\/\fR
+*Mer length
+.TP
+\fB\-b\fR, \fB\-\-bits\fR=\fI\,uint32\/\fR
+*Bits for value field
+.TP
+\fB\-q\fR, \fB\-\-min\-qual\-value\fR=\fI\,uint32\/\fR
+Min quality as an int
+.TP
+\fB\-Q\fR, \fB\-\-min\-qual\-char\fR=\fI\,string\/\fR
+Min quality as a ASCII character
+.TP
+\fB\-t\fR, \fB\-\-threads\fR=\fI\,uint32\/\fR
+Number of threads (1)
+.TP
+\fB\-o\fR, \fB\-\-output\fR=\fI\,path\/\fR
+Output file (combined_database)
+.TP
+\fB\-p\fR, \fB\-\-reprobe\fR=\fI\,int32\/\fR
+Maximum number of reprobes (126)
+.TP
+\fB\-U\fR, \fB\-\-usage\fR
+Usage
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+This message
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+Version
+.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/quorum_error_correct_reads.1 b/debian/mans/quorum_error_correct_reads.1
new file mode 100644
index 0000000..7b36aa3
--- /dev/null
+++ b/debian/mans/quorum_error_correct_reads.1
@@ -0,0 +1,81 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH QUORUM_ERROR_CORRECT_READS "1" "May 2017" "quorum_error_correct_reads 1.1.1" "User Commands"
+.SH NAME
+quorum_error_correct_reads \- error correct reads from a fastq file based on the k-mer frequencies
+.SH SYNOPSIS
+.B error_correct_reads
+[\fI\,options\/\fR] \fI\,db:path sequence:path+\/\fR
+.SH DESCRIPTION
+Error correct reads from a fastq file based on the k\-mer frequencies.
+.SS "Options (default value in (), *required):"
+.TP
+\fB\-t\fR, \fB\-\-thread\fR=\fI\,uint32\/\fR
+Number of threads (1)
+.TP
+\fB\-m\fR, \fB\-\-min\-count\fR=\fI\,uint32\/\fR
+Minimum count for a k\-mer to be considered "good" (1)
+.TP
+\fB\-s\fR, \fB\-\-skip\fR=\fI\,uint32\/\fR
+Number of bases to skip for start k\-mer (1)
+.TP
+\fB\-g\fR, \fB\-\-good\fR=\fI\,uint32\/\fR
+Number of good k\-mer in a row for anchor (2)
+.TP
+\fB\-a\fR, \fB\-\-anchor\-count\fR=\fI\,uint32\/\fR
+Minimum count for an anchor k\-mer (3)
+.TP
+\fB\-w\fR, \fB\-\-window\fR=\fI\,uint32\/\fR
+Size of window (10)
+.TP
+\fB\-e\fR, \fB\-\-error\fR=\fI\,uint32\/\fR
+Maximum number of error in a window (3)
+.TP
+\fB\-o\fR, \fB\-\-output\fR=\fI\,prefix\/\fR
+Output file prefix (error_corrected)
+.TP
+\fB\-\-contaminant\fR=\fI\,path\/\fR
+Jellyfish database of contaminant k\-mers
+.TP
+\fB\-\-trim\-contaminant\fR
+Trim reads containing contaminated k\-mers instead of discarding (false)
+.TP
+\fB\-\-homo\-trim\fR=\fI\,int32\/\fR
+Trim homo\-polymer run at the 3' end
+.TP
+\fB\-\-gzip\fR
+Gzip output file (false)
+.TP
+\fB\-M\fR, \fB\-\-no\-mmap\fR
+Do not memory map the input mer database (false)
+.TP
+\fB\-\-apriori\-error\-rate\fR=\fI\,double\/\fR
+Probability of a base being an error (0.01)
+.TP
+\fB\-\-poisson\-threshold\fR=\fI\,double\/\fR
+Error probability threshold in Poisson test (1.0e\-06)
+.TP
+\fB\-p\fR, \fB\-\-cutoff\fR=\fI\,uint32\/\fR
+Poisson cutoff when there are multiple choices
+.TP
+\fB\-q\fR, \fB\-\-qual\-cutoff\-value\fR=\fI\,uint32\/\fR
+Any base above with quality equal or greater is untouched when there are multiple choices
+.TP
+\fB\-Q\fR, \fB\-\-qual\-cutoff\-char\fR=\fI\,string\/\fR
+Any base above with quality equal or greater is untouched when there are multiple choices
+.TP
+\fB\-d\fR, \fB\-\-no\-discard\fR
+Do not discard reads, output a single N (false)
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Be verbose (false)
+.TP
+\fB\-U\fR, \fB\-\-usage\fR
+Usage
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+This message
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+Version
+.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/split_mate_pairs.1 b/debian/mans/split_mate_pairs.1
new file mode 100644
index 0000000..9fde399
--- /dev/null
+++ b/debian/mans/split_mate_pairs.1
@@ -0,0 +1,20 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH SPLIT_MATE_PAIRS "1" "May 2017" "split_mate_pairs 1.1.1" "User Commands"
+.SH NAME
+split_mate_pairs \- split fasta file in two
+.SH DESCRIPTION
+Split fasta file in two
+.PP
+Read fasta file from stdin and write sequence alternatively to two output files
+.SS "Options (default value in (), *required):"
+.TP
+\fB\-U\fR, \fB\-\-usage\fR
+Usage
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+This message
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+Version
+.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/rules b/debian/rules
new file mode 100755
index 0000000..7f584b9
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,15 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+
+%:
+ dh $@ --no-parallel
+
+override_dh_install:
+ dh_install
+ mkdir -p debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)
+ mv debian/$(DEBPKGNAME)/usr/share/adapter* debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)
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..f4a8d1d
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Guillaume Marçais and James A. Yorke and Aleksey Zimin
+ Title: "QuorUM: An Error Corrector for Illumina Reads"
+ Journal: PLoS One
+ Year: 2015
+ Volume: 10
+ Number: 6
+ Pages: e0130821
+ DOI: 10.1371/journal.pone.0130821
+ PMID: 26083032
+ URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130821
+ eprint: http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0130821&type=printable
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..e5b4d6e
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+
+https://github.com/gmarcais/Quorum/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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