[med-svn] r13122 - in trunk/packages/aragorn/trunk/debian: . man
Sascha Steinbiss
sascha-guest at alioth.debian.org
Sat Mar 2 20:00:26 UTC 2013
Author: sascha-guest
Date: 2013-03-02 20:00:25 +0000 (Sat, 02 Mar 2013)
New Revision: 13122
Removed:
trunk/packages/aragorn/trunk/debian/man/aragorn.1
trunk/packages/aragorn/trunk/debian/manpage.1.src
Modified:
trunk/packages/aragorn/trunk/debian/control
trunk/packages/aragorn/trunk/debian/rules
Log:
build man page from source tarball
Modified: trunk/packages/aragorn/trunk/debian/control
===================================================================
--- trunk/packages/aragorn/trunk/debian/control 2013-03-02 19:52:00 UTC (rev 13121)
+++ trunk/packages/aragorn/trunk/debian/control 2013-03-02 20:00:25 UTC (rev 13122)
@@ -3,7 +3,7 @@
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
-Build-Depends: debhelper (>= 9), hardening-includes
+Build-Depends: debhelper (>= 9), hardening-includes, asciidoc
Standards-Version: 3.9.4
Homepage: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/aragorn/trunk/
Deleted: trunk/packages/aragorn/trunk/debian/man/aragorn.1
===================================================================
--- trunk/packages/aragorn/trunk/debian/man/aragorn.1 2013-03-02 19:52:00 UTC (rev 13121)
+++ trunk/packages/aragorn/trunk/debian/man/aragorn.1 2013-03-02 20:00:25 UTC (rev 13122)
@@ -1,390 +0,0 @@
-'\" t
-.\" Title: aragorn
-.\" Author: [see the "AUTHORS" section]
-.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: 02/24/2013
-.\" Manual: \ \&
-.\" Source: \ \&
-.\" Language: English
-.\"
-.TH "ARAGORN" "1" "02/24/2013" "\ \&" "\ \&"
-.\" -----------------------------------------------------------------
-.\" * Define some portability stuff
-.\" -----------------------------------------------------------------
-.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.\" http://bugs.debian.org/507673
-.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
-.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.ie \n(.g .ds Aq \(aq
-.el .ds Aq '
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
-.SH "NAME"
-aragorn \- detect tRNA genes in nucleotide sequences
-.SH "SYNOPSIS"
-.sp
-\fBaragorn\fR [\fIOPTION\fR]\&... \fIFILE\fR
-.SH "OPTIONS"
-.PP
-\fB\-m\fR
-.RS 4
-Search for tmRNA genes\&.
-.RE
-.PP
-\fB\-t\fR
-.RS 4
-Search for tRNA genes\&. By default, all are detected\&. If one of
-\fB\-m\fR
-or
-\fB\-t\fR
-is specified, then the other is not detected unless specified as well\&.
-.RE
-.PP
-\fB\-mt\fR
-.RS 4
-Search for Metazoan mitochondrial tRNA genes\&. tRNA genes with introns not detected\&.
-\fB\-i\fR,
-\fB\-sr\fR
-switchs ignored\&. Composite Metazoan mitochondrial genetic code used\&.
-.RE
-.PP
-\fB\-mtmam\fR
-.RS 4
-Search for Mammalian mitochondrial tRNA genes\&.
-\fB\-i\fR,
-\fB\-sr\fR
-switchs ignored\&.
-\fB\-tv\fR
-switch set\&. Mammalian mitochondrial genetic code used\&.
-.RE
-.PP
-\fB\-mtx\fR
-.RS 4
-Same as
-\fB\-mt\fR
-but low scoring tRNA genes are not reported\&.
-.RE
-.PP
-\fB\-mtd\fR
-.RS 4
-Overlapping metazoan mitochondrial tRNA genes on opposite strands are reported\&.
-.RE
-.PP
-\fB\-gc\fR[\fInum\fR]
-.RS 4
-Use the GenBank transl_table = [\fInum\fR] genetic code\&. Individual modifications can be appended using
-\fI,BBB\fR=<aa> B = A,C,G, or T\&. <aa> is the three letter code for an amino\-acid\&. More than one modification can be specified\&. eg
-\fB\-gcvert\fR,aga=Trp,agg=Trp uses the Vertebrate Mitochondrial code and the codons AGA and AGG changed to Tryptophan\&.
-.RE
-.PP
-\fB\-gcstd\fR
-.RS 4
-Use standard genetic code\&.
-.RE
-.PP
-\fB\-gcmet\fR
-.RS 4
-Use composite Metazoan mitochondrial genetic code\&.
-.RE
-.PP
-\fB\-gcvert\fR
-.RS 4
-Use Vertebrate mitochondrial genetic code\&.
-.RE
-.PP
-\fB\-gcinvert\fR
-.RS 4
-Use Invertebrate mitochondrial genetic code\&.
-.RE
-.PP
-\fB\-gcyeast\fR
-.RS 4
-Use Yeast mitochondrial genetic code\&.
-.RE
-.PP
-\fB\-gcprot\fR
-.RS 4
-Use Mold/Protozoan/Coelenterate mitochondrial genetic code\&.
-.RE
-.PP
-\fB\-gcciliate\fR
-.RS 4
-Use Ciliate genetic code\&.
-.RE
-.PP
-\fB\-gcflatworm\fR
-.RS 4
-Use Echinoderm/Flatworm mitochondrial genetic code
-.RE
-.PP
-\fB\-gceuplot\fR
-.RS 4
-Use Euplotid genetic code\&.
-.RE
-.PP
-\fB\-gcbact\fR
-.RS 4
-Use Bacterial/Plant Chloroplast genetic code\&.
-.RE
-.PP
-\fB\-gcaltyeast\fR
-.RS 4
-Use alternative Yeast genetic code\&.
-.RE
-.PP
-\fB\-gcascid\fR
-.RS 4
-Use Ascidian Mitochondrial genetic code\&.
-.RE
-.PP
-\fB\-gcaltflat\fR
-.RS 4
-Use alternative Flatworm Mitochondrial genetic code\&.
-.RE
-.PP
-\fB\-gcblep\fR
-.RS 4
-Use Blepharisma genetic code\&.
-.RE
-.PP
-\fB\-gcchloroph\fR
-.RS 4
-Use Chlorophycean Mitochondrial genetic code\&.
-.RE
-.PP
-\fB\-gctrem\fR
-.RS 4
-Use Trematode Mitochondrial genetic code\&.
-.RE
-.PP
-\fB\-gcscen\fR
-.RS 4
-Use Scenedesmus obliquus Mitochondrial genetic code\&.
-.RE
-.PP
-\fB\-gcthraust\fR
-.RS 4
-Use Thraustochytrium Mitochondrial genetic code\&.
-.RE
-.PP
-\fB\-tv\fR
-.RS 4
-Do not search for mitochondrial TV replacement loop tRNA genes\&. Only relevant if
-\fB\-mt\fR
-used\&.
-.RE
-.PP
-\fB\-c7\fR
-.RS 4
-Search for tRNA genes with 7 base C\-loops only\&.
-.RE
-.PP
-\fB\-i\fR
-.RS 4
-Search for tRNA genes with introns in anticodon loop with maximum length 3000 bases\&. Minimum intron length is 0 bases\&. Ignored if
-\fB\-m\fR
-is specified\&.
-.RE
-.PP
-\fB\-i\fR[\fImax\fR]
-.RS 4
-Search for tRNA genes with introns in anticodon loop with maximum length [\fImax\fR] bases\&. Minimum intron length is 0 bases\&. Ignored if
-\fB\-m\fR
-is specified\&.
-.RE
-.PP
-\fB\-i\fR[\fImin\fR],[\fImax\fR]
-.RS 4
-Search for tRNA genes with introns in anticodon loop with maximum length [\fImax\fR] bases, and minimum length [\fImin\fR] bases\&. Ignored if
-\fB\-m\fR
-is specified\&.
-.RE
-.PP
-\fB\-io\fR
-.RS 4
-Same as
-\fB\-i\fR, but allow tRNA genes with long introns to overlap shorter tRNA genes\&.
-.RE
-.PP
-\fB\-if\fR
-.RS 4
-Same as
-\fB\-i\fR, but fix intron between positions 37 and 38 on C\-loop (one base after anticodon)\&.
-.RE
-.PP
-\fB\-ifo\fR
-.RS 4
-Same as
-\fB\-if\fR
-and
-\fB\-io\fR
-combined\&.
-.RE
-.PP
-\fB\-ir\fR
-.RS 4
-Same as
-\fB\-i\fR, but report tRNA genes with minimum length [\fImin\fR] bases rather than search for tRNA genes with minimum length [\fImin\fR] bases\&. With this switch, [\fImin\fR] acts as an output filter, minimum intron length for searching is still 0 bases\&.
-.RE
-.PP
-\fB\-c\fR
-.RS 4
-Assume that each sequence has a circular topology\&. Search wraps around each end\&. Default setting\&.
-.RE
-.PP
-\fB\-l\fR
-.RS 4
-Assume that each sequence has a linear topology\&. Search does not wrap\&.
-.RE
-.PP
-\fB\-d\fR
-.RS 4
-Double\&. Search both strands of each sequence\&. Default setting\&.
-.RE
-.PP
-\fB\-s\fR or \fB\-s+\fR
-.RS 4
-Single\&. Do not search the complementary (antisense) strand of each sequence\&.
-.RE
-.PP
-\fB\-sc\fR or \fB\-s\-\fR
-.RS 4
-Single complementary\&. Do not search the sense strand of each sequence\&.
-.RE
-.PP
-\fB\-ps\fR
-.RS 4
-Lower scoring thresholds to 95% of default levels\&.
-.RE
-.PP
-\fB\-ps\fR[\fInum\fR]
-.RS 4
-Change scoring thresholds to [\fInum\fR] percent of default levels\&.
-.RE
-.PP
-\fB\-rp\fR
-.RS 4
-Flag possible pseudogenes (score < 100 or tRNA anticodon loop <> 7 bases long)\&. Note that genes with score < 100 will not be detected or flagged if scoring thresholds are not also changed to below 100% (see \-ps switch)\&.
-.RE
-.PP
-\fB\-seq\fR
-.RS 4
-Print out primary sequence\&.
-.RE
-.PP
-\fB\-br\fR
-.RS 4
-Show secondary structure of tRNA gene primary sequence using round brackets\&.
-.RE
-.PP
-\fB\-fasta\fR
-.RS 4
-Print out primary sequence in fasta format\&.
-.RE
-.PP
-\fB\-fo\fR
-.RS 4
-Print out primary sequence in fasta format only (no secondary structure)\&.
-.RE
-.PP
-\fB\-fon\fR
-.RS 4
-Same as
-\fB\-fo\fR, with sequence and gene numbering in header\&.
-.RE
-.PP
-\fB\-fos\fR
-.RS 4
-Same as
-\fB\-fo\fR, with no spaces in header\&.
-.RE
-.PP
-\fB\-fons\fR
-.RS 4
-Same as
-\fB\-fo\fR, with sequence and gene numbering, but no spaces\&.
-.RE
-.PP
-\fB\-w\fR
-.RS 4
-Print out in Batch mode\&.
-.RE
-.PP
-\fB\-ss\fR
-.RS 4
-Use the stricter canonical 1\-2 bp spacer1 and 1 bp spacer2\&. Ignored if
-\fB\-mt\fR
-set\&. Default is to allow 3 bp spacer1 and 0\-2 bp spacer2, which may degrade selectivity\&.
-.RE
-.PP
-\fB\-v\fR
-.RS 4
-Verbose\&. Prints out information during search to STDERR\&.
-.RE
-.PP
-\fB\-a\fR
-.RS 4
-Print out tRNA domain for tmRNA genes\&.
-.RE
-.PP
-\fB\-a7\fR
-.RS 4
-Restrict tRNA astem length to a maximum of 7 bases
-.RE
-.PP
-\fB\-aa\fR
-.RS 4
-Display message if predicted iso\-acceptor species does not match species in sequence name (if present)\&.
-.RE
-.PP
-\fB\-j\fR
-.RS 4
-Display 4\-base sequence on 3\*(Aq end of astem regardless of predicted amino\-acyl acceptor length\&.
-.RE
-.PP
-\fB\-jr\fR
-.RS 4
-Allow some divergence of 3\*(Aq amino\-acyl acceptor sequence from NCCA\&.
-.RE
-.PP
-\fB\-jr4\fR
-.RS 4
-Allow some divergence of 3\*(Aq amino\-acyl acceptor sequence from NCCA, and display 4 bases\&.
-.RE
-.PP
-\fB\-q\fR
-.RS 4
-Dont print configuration line (which switchs and files were used)\&.
-.RE
-.PP
-\fB\-rn\fR
-.RS 4
-Repeat sequence name before summary information\&.
-.RE
-.PP
-\fB\-O\fR [\fIoutfile\fR]
-.RS 4
-Print output to
-\fI\&. If [\*(Aqoutfile\fR] already exists, it is overwritten\&. By default all output goes to stdout\&.
-.RE
-.SH "DESCRIPTION"
-.sp
-aragorn detects tRNA, mtRNA, and tmRNA genes\&. A minimum requirement is at least a 32 bit compiler architecture (variable types int and unsigned int are at least 4 bytes long)\&.
-.sp
-[\fIFILE\fR] is assumed to contain one or more sequences in FASTA format\&. Results of the search are printed to STDOUT\&. All switches are optional and case\-insensitive\&. Unless \-i is specified, tRNA genes containing introns are not detected\&.
-.SH "AUTHORS"
-.sp
-Bjorn Canback <bcanback at acgt\&.se>, Dean Laslett <gaiaquark at gmail\&.com>
-.SH "REFERENCES"
-.sp
-Laslett, D\&. and Canback, B\&. (2004) ARAGORN, a program for the detection of transfer RNA and transfer\-messenger RNA genes in nucleotide sequences Nucleic Acids Research, 32;11\-16
-.sp
-Laslett, D\&. and Canback, B\&. (2008) ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences Bioinformatics, 24(2); 172\-175\&.
Deleted: trunk/packages/aragorn/trunk/debian/manpage.1.src
===================================================================
--- trunk/packages/aragorn/trunk/debian/manpage.1.src 2013-03-02 19:52:00 UTC (rev 13121)
+++ trunk/packages/aragorn/trunk/debian/manpage.1.src 2013-03-02 20:00:25 UTC (rev 13122)
@@ -1,270 +0,0 @@
-ARAGORN(1)
-==========
-
-NAME
-----
-
-aragorn - detect tRNA genes in nucleotide sequences
-
-
-SYNOPSIS
---------
-
-*aragorn* ['OPTION']... 'FILE'
-
-
-OPTIONS
--------
-
-*-m*::
- Search for tmRNA genes.
-
-*-t*::
- Search for tRNA genes.
- By default, all are detected. If one of
- *-m* or *-t* is specified, then the other
- is not detected unless specified as well.
-*-mt*::
- Search for Metazoan mitochondrial tRNA genes.
- tRNA genes with introns not detected. *-i*, *-sr* switchs
- ignored. Composite Metazoan mitochondrial
- genetic code used.
-
-*-mtmam*::
- Search for Mammalian mitochondrial tRNA
- genes. *-i*, *-sr* switchs ignored. *-tv* switch set.
- Mammalian mitochondrial genetic code used.
-
-*-mtx*::
- Same as *-mt* but low scoring tRNA genes are
- not reported.
-
-*-mtd*::
- Overlapping metazoan mitochondrial tRNA genes
- on opposite strands are reported.
-
-*-gc*['num']::
- Use the GenBank transl_table = ['num'] genetic code.
- Individual modifications can be appended using
- ',BBB'=<aa> B = A,C,G, or T. <aa> is the three letter
- code for an amino-acid. More than one modification
- can be specified. eg *-gcvert*,aga=Trp,agg=Trp uses
- the Vertebrate Mitochondrial code and the codons
- AGA and AGG changed to Tryptophan.
-
-*-gcstd*::
- Use standard genetic code.
-*-gcmet*::
- Use composite Metazoan mitochondrial genetic code.
-*-gcvert*::
- Use Vertebrate mitochondrial genetic code.
-*-gcinvert*::
- Use Invertebrate mitochondrial genetic code.
-*-gcyeast*::
- Use Yeast mitochondrial genetic code.
-*-gcprot*::
- Use Mold/Protozoan/Coelenterate mitochondrial genetic code.
-*-gcciliate*::
- Use Ciliate genetic code.
-*-gcflatworm*::
- Use Echinoderm/Flatworm mitochondrial genetic code
-*-gceuplot*::
- Use Euplotid genetic code.
-*-gcbact*::
- Use Bacterial/Plant Chloroplast genetic code.
-*-gcaltyeast*::
- Use alternative Yeast genetic code.
-*-gcascid*::
- Use Ascidian Mitochondrial genetic code.
-*-gcaltflat*::
- Use alternative Flatworm Mitochondrial genetic code.
-*-gcblep*::
- Use Blepharisma genetic code.
-*-gcchloroph*::
- Use Chlorophycean Mitochondrial genetic code.
-*-gctrem*::
- Use Trematode Mitochondrial genetic code.
-*-gcscen*::
- Use Scenedesmus obliquus Mitochondrial genetic code.
-*-gcthraust*::
- Use Thraustochytrium Mitochondrial genetic code.
-
-*-tv*::
- Do not search for mitochondrial TV replacement loop tRNA genes. Only relevant if *-mt* used.
-
-*-c7*::
- Search for tRNA genes with 7 base C-loops only.
-
-*-i*::
- Search for tRNA genes with introns in
- anticodon loop with maximum length 3000
- bases. Minimum intron length is 0 bases.
- Ignored if *-m* is specified.
-
-*-i*['max']::
- Search for tRNA genes with introns in
- anticodon loop with maximum length ['max']
- bases. Minimum intron length is 0 bases.
- Ignored if *-m* is specified.
-
-*-i*['min'],['max']::
- Search for tRNA genes with introns in
- anticodon loop with maximum length ['max']
- bases, and minimum length ['min'] bases.
- Ignored if *-m* is specified.
-
-*-io*::
- Same as *-i*, but allow tRNA genes with long
- introns to overlap shorter tRNA genes.
-
-*-if*::
- Same as *-i*, but fix intron between positions
- 37 and 38 on C-loop (one base after anticodon).
-
-*-ifo*::
- Same as *-if* and *-io* combined.
-
-*-ir*::
- Same as *-i*, but report tRNA genes with minimum
- length ['min'] bases rather than search for
- tRNA genes with minimum length ['min'] bases.
- With this switch, ['min'] acts as an output filter,
- minimum intron length for searching is still 0 bases.
-
-*-c*::
- Assume that each sequence has a circular
- topology. Search wraps around each end.
- Default setting.
-
-*-l*::
- Assume that each sequence has a linear
- topology. Search does not wrap.
-
-*-d*::
- Double. Search both strands of each
- sequence. Default setting.
-
-*-s* or *-s+*::
- Single. Do not search the complementary
- (antisense) strand of each sequence.
-
-*-sc* or *-s-*::
- Single complementary. Do not search the sense
- strand of each sequence.
-
-*-ps*::
- Lower scoring thresholds to 95% of default levels.
-
-*-ps*['num']::
- Change scoring thresholds to ['num'] percent of
- default levels.
-
-*-rp*::
- Flag possible pseudogenes (score < 100 or tRNA anticodon
- loop <> 7 bases long). Note that genes with score < 100
- will not be detected or flagged if scoring thresholds are not
- also changed to below 100% (see -ps switch).
-
-*-seq*::
- Print out primary sequence.
-
-*-br*::
- Show secondary structure of tRNA gene primary sequence
- using round brackets.
-
-*-fasta*::
- Print out primary sequence in fasta format.
-*-fo*::
- Print out primary sequence in fasta format only
- (no secondary structure).
-
-*-fon*::
- Same as *-fo*, with sequence and gene numbering in header.
-
-*-fos*::
- Same as *-fo*, with no spaces in header.
-
-*-fons*::
- Same as *-fo*, with sequence and gene numbering, but no
- spaces.
-
-*-w*::
- Print out in Batch mode.
-
-*-ss*::
- Use the stricter canonical 1-2 bp spacer1 and
- 1 bp spacer2. Ignored if *-mt* set. Default is to
- allow 3 bp spacer1 and 0-2 bp spacer2, which may
- degrade selectivity.
-
-*-v*::
- Verbose. Prints out information during
- search to STDERR.
-
-*-a*::
- Print out tRNA domain for tmRNA genes.
-
-*-a7*::
- Restrict tRNA astem length to a maximum of 7 bases
-
-*-aa*::
- Display message if predicted iso-acceptor species
- does not match species in sequence name (if present).
-
-*-j*::
- Display 4-base sequence on 3' end of astem
- regardless of predicted amino-acyl acceptor length.
-
-*-jr*::
- Allow some divergence of 3' amino-acyl acceptor
- sequence from NCCA.
-
-*-jr4*::
- Allow some divergence of 3' amino-acyl acceptor
- sequence from NCCA, and display 4 bases.
-
-*-q*::
- Dont print configuration line (which switchs
- and files were used).
-*-rn*::
- Repeat sequence name before summary information.
-
-*-O* ['outfile']::
- Print output to ['outfile]'. If ['outfile']
- already exists, it is overwritten. By default
- all output goes to stdout.
-
-DESCRIPTION
------------
-
-aragorn detects tRNA, mtRNA, and tmRNA genes.
-A minimum requirement is at least a 32 bit compiler architecture
-(variable types int and unsigned int are at least 4 bytes long).
-
-['FILE'] is assumed to contain one or more sequences
-in FASTA format. Results of the search are printed to
-STDOUT. All switches are optional and case-insensitive.
-Unless -i is specified, tRNA genes containing introns
-are not detected.
-
-
-AUTHORS
-------
-
-Bjorn Canback <bcanback at acgt.se>, Dean Laslett <gaiaquark at gmail.com>
-
-
-REFERENCES
-----------
-
-Laslett, D. and Canback, B. (2004) ARAGORN, a
-program for the detection of transfer RNA and transfer-messenger
-RNA genes in nucleotide sequences
-Nucleic Acids Research, 32;11-16
-
-Laslett, D. and Canback, B. (2008) ARWEN: a
-program to detect tRNA genes in metazoan mitochondrial
-nucleotide sequences
-Bioinformatics, 24(2); 172-175.
-
-
Modified: trunk/packages/aragorn/trunk/debian/rules
===================================================================
--- trunk/packages/aragorn/trunk/debian/rules 2013-03-02 19:52:00 UTC (rev 13121)
+++ trunk/packages/aragorn/trunk/debian/rules 2013-03-02 20:00:25 UTC (rev 13122)
@@ -19,6 +19,7 @@
override_dh_auto_build:
$(CC) $(CFLAGS) $(LDFLAGS) -O3 -ffast-math -finline-functions -o aragorn *.c
+ a2x --doctype manpage --format manpage manpage.1.src --destination-dir=$(DESTDIR)/man
override_dh_auto_install:
mkdir -p $(DESTDIR)/usr/bin
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