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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> + Aleksey Zimin <[email protected]> +Source: https://github.com/gmarcais/Quorum/releases + +Files: * +Copyright: 2012-2016 Guillaume Marçais <[email protected]>, + Aleksey Zimin <[email protected]>, + Copyright: 2012, Genome group at University of Maryland +License: GPL-3+ + +Files: unit_tests/gtest +Copyright: 2005, 2006, 2008 Zhanyong Wan <[email protected]> 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 <[email protected]> +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) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/quorum.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
