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commit c4308ec9a7f6a3e90e5140cc9b01710eae8f369d Author: Andreas Tille <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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: [email protected] +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 <[email protected]> +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 [email protected]\-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 [email protected]\-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 [email protected]\-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 <[email protected]> +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 + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/segemehl.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
