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-packag...@lists.alioth.debian.org> Uploaders: Sascha Steinbiss <steinb...@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@acgt\&.se>, Dean Laslett <gaiaquark@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 <bcanb...@acgt.se>, Dean Laslett <gaiaqu...@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 _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit