[med-svn] [segemehl] 02/02: Inject packaging
Andreas Tille
tille at debian.org
Mon Jun 20 11:36:14 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository segemehl.
commit c4308ec9a7f6a3e90e5140cc9b01710eae8f369d
Author: Andreas Tille <tille at debian.org>
Date: Mon Jun 20 13:33:59 2016 +0200
Inject packaging
---
debian/changelog | 5 ++
debian/clean | 1 +
debian/compat | 1 +
debian/control | 27 +++++++
debian/copyright | 19 +++++
debian/install | 1 +
debian/manpages | 1 +
debian/mans/lack.x.1 | 62 ++++++++++++++++
debian/mans/segemehl.x.1 | 163 +++++++++++++++++++++++++++++++++++++++++
debian/mans/testrealign.x.1 | 56 ++++++++++++++
debian/patches/hardening.patch | 16 ++++
debian/patches/series | 1 +
debian/rules | 6 ++
debian/source/format | 1 +
debian/upstream/metadata | 33 +++++++++
debian/watch | 5 ++
16 files changed, 398 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..e37eb63
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+segemehl (0.2.0+dfsg-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Mon, 20 Jun 2016 12:09:31 +0200
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..91796e7
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+segemehl/*.x
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..e2d4ed6
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,27 @@
+Source: segemehl
+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),
+ libncurses-dev,
+ zlib1g-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/segemehl.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/segemehl.git
+Homepage: http://www.bioinf.uni-leipzig.de/Software/segemehl/
+
+Package: segemehl
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: short read mapping with gaps
+ segemehl is a software to map short sequencer reads to reference
+ genomes. Unlike other methods, segemehl is able to detect not only
+ mismatches but also insertions and deletions. Furthermore, segemehl
+ is not limited to a specific read length and is able to mapprimer-
+ or polyadenylation contaminated reads correctly. segemehl implements
+ a matching strategy based on enhanced suffix arrays (ESA). Segemehl
+ now supports the SAM format, reads gziped queries to save both disk
+ and memory space and allows bisulfite sequencing mapping and split
+ read mapping.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..7f007c9
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,19 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: segemehl
+Upstream-Contact: steve at bioinf.uni-leipzig.de
+Source: http://www.bioinf.uni-leipzig.de/Software/segemehl/
+Files-Excluded: */cscope.out
+ *.o
+ *~
+ *.SUNOS
+
+Files: *
+Copyright: 2008-2015 Bioinformatik Leipzig
+License: non-commercial
+ SEGEMEHL is free software for non-commercial use
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: to_be_clarified
+ Ask upstream for free license and choose the same for
+ the packaging.
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..259b516
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+segemehl/*.x usr/bin
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..4f4649b
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*.1
diff --git a/debian/mans/lack.x.1 b/debian/mans/lack.x.1
new file mode 100644
index 0000000..c14c1a4
--- /dev/null
+++ b/debian/mans/lack.x.1
@@ -0,0 +1,62 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH LACK.X "1" "June 2016" "lack.x 0.2.0" "User Commands"
+.SH NAME
+lack.x \- Remapping of unmapped reads
+.SH SYNOPSIS
+.B lack.x
+[\-s] \fB\-d\fR <file> [<file> ...] \fB\-q\fR <file> [<file> ...] [\-o <string>] \fB\-r\fR <file> [\-u <file>] [\-t <n>] [\-A <n>] [\-W <n>] [\-U <n>] [\-Z <n>] [\-M <n>]
+.SH DESCRIPTION
+This program belongs to the segemehl package (see segemehl(1))
+.P
+Segemehl is a software to map short sequencer reads to reference
+genomes. Unlike other methods, segemehl is able to detect not only
+mismatches but also insertions and deletions. Furthermore, segemehl
+is not limited to a specific read length and is able to mapprimer-
+or polyadenylation contaminated reads correctly. segemehl implements
+a matching strategy based on enhanced suffix arrays (ESA). Segemehl
+now supports the SAM format, reads gziped queries to save both disk
+and memory space and allows bisulfite sequencing mapping and split
+read mapping.
+.SH OPTIONS
+.TP
+\fB\-d\fR, \fB\-\-database\fR <file> [<file> ...]
+list of path/filename(s) of database sequence(s)
+.TP
+\fB\-q\fR, \fB\-\-query\fR <file> [<file> ...]
+path/filename of alignment file
+.TP
+\fB\-o\fR, \fB\-\-outfile\fR <string>
+outputfile (default:none)
+.TP
+\fB\-r\fR, \fB\-\-remapfilename\fR <file>
+filename for reads to be remapped (default:none)
+.TP
+\fB\-u\fR, \fB\-\-nomatchfilename\fR <file>
+filename for unmatched reads (default:none)
+.TP
+\fB\-t\fR, \fB\-\-threads\fR <n>
+start <n> threads for remapping (default:1)
+.TP
+\fB\-s\fR, \fB\-\-silent\fR
+shut up!
+.TP
+\fB\-A\fR, \fB\-\-accuracy\fR <n>
+min percentage of matches per read in semi\-global alignment (default:90)
+.TP
+\fB\-W\fR, \fB\-\-minsplicecover\fR <n>
+min coverage for spliced transcripts (default:80)
+.TP
+\fB\-U\fR, \fB\-\-minfragscore\fR <n>
+min score of a spliced fragment (default:5)
+.TP
+\fB\-Z\fR, \fB\-\-minfraglen\fR <n>
+min length of a spliced fragment (default:5)
+.TP
+\fB\-M\fR, \fB\-\-maxdist\fR <n>
+max number of distant sites to consider, 0 to disable (default:100)
+.SH BUGS
+Please report bugs to christian at bioinf.uni\-leipzig.de
+.SH AUTHOR
+This software was written by Christian Otto and others at Bioinformatik Leipzig
+.P
+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/segemehl.x.1 b/debian/mans/segemehl.x.1
new file mode 100644
index 0000000..4294559
--- /dev/null
+++ b/debian/mans/segemehl.x.1
@@ -0,0 +1,163 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH SEGEMEHL.X "1" "June 2016" "segemehl.x 0.2.0" "User Commands"
+.SH NAME
+segemehl.x \- Heuristic mapping of short sequences
+.SH SYNOPSIS
+.B segemehl.x
+[\-sbcKVTYCO] \fB\-d\fR <file> [<file>] [\-q <file>] [\-p <file>] [\-i <file>] [\-j <file>] [\-x <file>] [\-y <file>] [\-B <string>] [\-F <n>] [\-m <n>] [\-t <n>] [\-o <string>] [\-u <file>] [\-D <n>] [\-J <n>]
+[\-E <double>] [\-w <double>] [\-M <n>] [\-r <n>] [\-S] [\-\-nohead] [\-e <n>] [\-n <n>] [\-X <n>] [\-A <n>] [\-W <n>] [\-U <n>] [\-Z <n>] [\-l <f>] [\-H] [\-\-showalign] [\-P <string>] [\-Q <string>]
+[\-R <n>] [\-I <n>]
+.SH DESCRIPTION
+Segemehl is a software to map short sequencer reads to reference
+genomes. Unlike other methods, segemehl is able to detect not only
+mismatches but also insertions and deletions. Furthermore, segemehl
+is not limited to a specific read length and is able to mapprimer-
+or polyadenylation contaminated reads correctly. segemehl implements
+a matching strategy based on enhanced suffix arrays (ESA). Segemehl
+now supports the SAM format, reads gziped queries to save both disk
+and memory space and allows bisulfite sequencing mapping and split
+read mapping.
+.SH OPTIONS
+.SS Input options
+.TP
+\fB\-d\fR, \fB\-\-database\fR <file> [<file>]
+list of path/filename(s) of database sequence(s)
+.TP
+\fB\-q\fR, \fB\-\-query\fR <file>
+path/filename of query sequences (default:none)
+.TP
+\fB\-p\fR, \fB\-\-mate\fR <file>
+path/filename of mate pair sequences (default:none)
+.TP
+\fB\-i\fR, \fB\-\-index\fR <file>
+path/filename of db index (default:none)
+.TP
+\fB\-j\fR, \fB\-\-index2\fR <file>
+path/filename of second db index (default:none)
+.TP
+\fB\-x\fR, \fB\-\-generate\fR <file>
+generate db index and store to disk (default:none)
+.TP
+\fB\-y\fR, \fB\-\-generate2\fR <file>
+generate second db index and store to disk (default:none)
+.TP
+\fB\-B\fR, \fB\-\-filebins\fR <string>
+file bins with basename <string> for easier data handling (default:none)
+.TP
+\fB\-F\fR, \fB\-\-bisulfite\fR <n>
+bisulfite mapping with methylC\-seq/Lister et al. (=1) or bs\-seq/Cokus et al. protocol (=2) (default:0)
+.SS General options
+.TP
+\fB\-m\fR, \fB\-\-minsize\fR <n>
+minimum size of queries (default:12)
+.TP
+\fB\-s\fR, \fB\-\-silent\fR
+shut up!
+.TP
+\fB\-b\fR, \fB\-\-brief\fR
+brief output
+.TP
+\fB\-c\fR, \fB\-\-checkidx\fR
+check index
+.TP
+\fB\-t\fR, \fB\-\-threads\fR <n>
+start <n> threads (default:1)
+.TP
+\fB\-o\fR, \fB\-\-outfile\fR <string>
+outputfile (default:none)
+.TP
+\fB\-u\fR, \fB\-\-nomatchfilename\fR <file>
+filename for unmatched reads (default:none)
+.SS Options for SEEDPARAMS
+.TP
+\fB\-D\fR, \fB\-\-differences\fR <n>
+search seeds initially with <n> differences (default:1)
+.TP
+\fB\-J\fR, \fB\-\-jump\fR <n>
+search seeds with jump size <n> (0=automatic) (default:0)
+.TP
+\fB\-E\fR, \fB\-\-evalue\fR <double>
+max evalue (default:5.000000)
+.TP
+\fB\-w\fR, \fB\-\-maxsplitevalue\fR <double>
+max evalue for splits (default:50.000000)
+.TP
+\fB\-M\fR, \fB\-\-maxinterval\fR <n>
+maximum width of a suffix array interval, i.e. a query seed will be omitted if it matches more than <n> times (default:100)
+.TP
+\fB\-r\fR, \fB\-\-maxout\fR <n>
+maximum number of alignments that will be reported. If set to zero, all alignments will be reported (default:0)
+.TP
+\fB\-S\fR, \fB\-\-splits\fR
+detect split/spliced reads (default:none)
+.TP
+\fB\-K\fR, \fB\-\-SEGEMEHL\fR
+output SEGEMEHL format (needs to be selected for brief)
+.TP
+\fB\-V\fR, \fB\-\-MEOP\fR
+output MEOP field for easier variance calling in SAM (XE:Z:)
+.TP
+\fB\-\-nohead\fR
+do not output header
+.SS Options for SEEDEXTENSIONPARAMS
+.TP
+\fB\-e\fR, \fB\-\-extensionscore\fR <n>
+score of a match during extension (default:2)
+.TP
+\fB\-n\fR, \fB\-\-extensionpenalty\fR <n>
+penalty for a mismatch during extension (default:4)
+.TP
+\fB\-X\fR, \fB\-\-dropoff\fR <n>
+dropoff parameter for extension (default:8)
+.SS Options for ALIGNPARAMS
+.TP
+\fB\-A\fR, \fB\-\-accuracy\fR <n>
+min percentage of matches per read in semi\-global alignment (default:90)
+.TP
+\fB\-W\fR, \fB\-\-minsplicecover\fR <n>
+min coverage for spliced transcripts (default:80)
+.TP
+\fB\-U\fR, \fB\-\-minfragscore\fR <n>
+min score of a spliced fragment (default:18)
+.TP
+\fB\-Z\fR, \fB\-\-minfraglen\fR <n>
+min length of a spliced fragment (default:20)
+.TP
+\fB\-l\fR, \fB\-\-splicescorescale\fR <f>
+report spliced alignment with score s only if <f>*s is larger than next best spliced alignment (default:1.000000)
+.TP
+\fB\-H\fR, \fB\-\-hitstrategy\fR
+report only best scoring hits (=1) or all (=0) (default:1)
+.TP
+\fB\-\-showalign\fR
+show alignments
+.TP
+\fB\-P\fR, \fB\-\-prime5\fR <string>
+add 5' adapter (default:none)
+.TP
+\fB\-Q\fR, \fB\-\-prime3\fR <string>
+add 3' adapter (default:none)
+.TP
+\fB\-R\fR, \fB\-\-clipacc\fR <n>
+clipping accuracy (default:70)
+.TP
+\fB\-T\fR, \fB\-\-polyA\fR
+clip polyA tail
+.TP
+\fB\-Y\fR, \fB\-\-autoclip\fR
+autoclip unknown 3prime adapter
+.TP
+\fB\-C\fR, \fB\-\-hardclip\fR
+enable hard clipping
+.TP
+\fB\-O\fR, \fB\-\-order\fR
+sorts the output by chromsome and position (might take a while!)
+.TP
+\fB\-I\fR, \fB\-\-maxinsertsize\fR <n>
+maximum size of the inserts (paired end) (default:5000)
+.SH BUGS
+Please report bugs to steve at bioinf.uni\-leipzig.de
+.SH AUTHOR
+This software was written by Christian Otto and others at Bioinformatik Leipzig
+.P
+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/testrealign.x.1 b/debian/mans/testrealign.x.1
new file mode 100644
index 0000000..05a8248
--- /dev/null
+++ b/debian/mans/testrealign.x.1
@@ -0,0 +1,56 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH TESTREALIGN.X "1" "June 2016" "testrealign.x 0.2.0" "User Commands"
+.SH NAME
+testrealign.x \- Heuristic mapping of short sequences
+.SH SYNOPSIS
+.B testrealign.x
+[\-Evn] \fB\-d\fR <file> [<file> ...] \fB\-q\fR <file> [<file> ...] [\-t <n>] [\-U <file>] [\-T <file>] [\-o <file>] [\-M <n>]
+.SH DESCRIPTION
+This program belongs to the segemehl package (see segemehl(1))
+.P
+Segemehl is a software to map short sequencer reads to reference
+genomes. Unlike other methods, segemehl is able to detect not only
+mismatches but also insertions and deletions. Furthermore, segemehl
+is not limited to a specific read length and is able to mapprimer-
+or polyadenylation contaminated reads correctly. segemehl implements
+a matching strategy based on enhanced suffix arrays (ESA). Segemehl
+now supports the SAM format, reads gziped queries to save both disk
+and memory space and allows bisulfite sequencing mapping and split
+read mapping.
+.SH OPTIONS
+.TP
+\fB\-d\fR, \fB\-\-database\fR <file> [<file> ...]
+list of path/filename(s) of database sequence(s)
+.TP
+\fB\-q\fR, \fB\-\-query\fR <file> [<file> ...]
+path/filename of alignment file
+.TP
+\fB\-E\fR, \fB\-\-expand\fR
+expand
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+verbose
+.TP
+\fB\-n\fR, \fB\-\-norealign\fR
+do not realign
+.TP
+\fB\-t\fR, \fB\-\-threads\fR <n>
+start <n> threads for realigning (default:1)
+.TP
+\fB\-U\fR, \fB\-\-splitfile\fR <file>
+path/filename of the split bedfile (default:"splicesites.bed")
+.TP
+\fB\-T\fR, \fB\-\-transfile\fR <file>
+path/filename of bed files containing trans\-split (default:"transrealigned.bed")
+.TP
+\fB\-o\fR, \fB\-\-outfile\fR <file>
+path/filename of output sam file (default:none)
+.TP
+\fB\-M\fR, \fB\-\-maxdist\fR <n>
+max number of distant sites to consider, 0 to disable (default:100)
+.SH BUGS
+Please report bugs to steve at bioinf.uni\-leipzig.de
+.SH AUTHOR
+This software was written by Christian Otto and others at Bioinformatik Leipzig
+.P
+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/patches/hardening.patch b/debian/patches/hardening.patch
new file mode 100644
index 0000000..69883f1
--- /dev/null
+++ b/debian/patches/hardening.patch
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 20 Jun 2016 12:09:31 +0200
+Description: Propagate hardening options
+
+--- a/segemehl/Makefile
++++ b/segemehl/Makefile
+@@ -1,7 +1,7 @@
+ CC=gcc
+ LD=${CC}
+- CFLAGS= -Wall -pedantic -std=c99 -g -O3 -DFIXINSMALL -DFIXINBACKSPLICE -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Isrc -Ilibs -Ilibs/sufarray -Lsrc
+- LDFLAGS= -lm -lpthread -lz -lncurses
++ CFLAGS+= -Wall -pedantic -std=c99 -g -O3 -DFIXINSMALL -DFIXINBACKSPLICE -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Isrc -Ilibs -Ilibs/sufarray -Lsrc
++ LDFLAGS+= -lm -lpthread -lz -lncurses
+ CTAGS=ctags > tags
+ LIBS=-lob -lm -lpthread
+
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..749392b
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+%:
+ dh $@ --sourcedirectory=segemehl
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..c7dba92
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,33 @@
+Reference:
+ - Author: Steve Hoffmann and Christian Otto and Stefan Kurtz and Cynthia M. Sharma and Philipp Khaitovich and Jörg Vogel and Peter F. Stadler and Jörg Hackermüller
+ Title: Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures
+ Journal: PLoS Comput Biol
+ Year: 2009
+ Volume: 5
+ Number: 9
+ Pages: e1000502
+ DOI: 10.1371/journal.pcbi.1000502
+ PMID: 19750212
+ URL: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000502
+ eprint: http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1000502.PDF
+ - Author: Steve Hoffmann and Christian Otto and Gero Doose and Andrea Tanzer and David Langenberger and Sabina Christ and Manfred Kunz and Lesca M Holdt and Daniel Teupser and Jörg Hackermüller and Peter F Stadler
+ Title: A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
+ Journal: Genome Biology
+ Year: 2014
+ Volume: 15
+ Pages: R34
+ DOI: 10.1186/gb-2014-15-2-r34
+ PMID: 24512684
+ URL: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-2-r34
+ eprint: https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2014-15-2-r34
+ - Author: Christian Otto and Peter F. Stadler and Steve Hoffmann
+ Title: Fast and sensitive mapping of bisulfite-treated sequencing data
+ Journal: Bioinformatics
+ Year: 2012
+ Volume: 28
+ Number: 13
+ Pages: 1698-704
+ DOI: 10.1093/bioinformatics/bts254
+ PMID: 22581174
+ URL: http://bioinformatics.oxfordjournals.org/content/28/13/1698
+ eprint: http://bioinformatics.oxfordjournals.org/content/28/13/1698.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..c6d0afb
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,5 @@
+version=3
+
+opts="uversionmangle=s/_/./g,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ http://www.bioinf.uni-leipzig.de/Software/segemehl/ .*/segemehl_(\d[_.\d]+)\.tar\.gz
+
--
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