debian/copyright

@@ -39,7 +39,7 @@ Copyright: (c) 2003-2009 Gordon Gremme <gordon@gremme.org>
            (c) 2003-2008 Center for Bioinformatics, University of Hamburg
 License: ISC
 
-File: src/gth/editoperation.h
+Files: src/gth/editoperation.h
 Copyright: (c) 2003-2009 Gordon Gremme <gordon@gremme.org>
            (c) 2003      Stefan Kurtz <kurtz@zbh.uni-hamburg.de>
            (c) 2003-2007 Center for Bioinformatics, University of Hamburg

debian/genomethreader.manpages

+debian/man/*.1

debian/man_src/gth.1.adoc

+# gth(1)
+
+## NAME
+
+gth - calculate genome structures
+
+## SYNOPSIS
+
+*gth* [option ...] -genomic file [...] -cdna file [...] -protein file [...]
+
+## DESCRIPTION
+
+Computes similarity-based gene structure predictions (spliced alignments)
+using cDNA/EST and/or protein sequences and assemble the resulting spliced
+alignments to consensus spliced alignments.
+
+## OPTIONS
+
+-genomic          specify input files containing genomic sequences
+                  mandatory option
+-cdna             specify input files containing cDNA/EST sequences
+-protein          specify input files containing protein sequences
+-species          specify species to select splice site model which is most
+                  appropriate; possible species:
+                  "human"
+                  "mouse"
+                  "rat"
+                  "chicken"
+                  "drosophila"
+                  "nematode"
+                  "fission_yeast"
+                  "aspergillus"
+                  "arabidopsis"
+                  "maize"
+                  "rice"
+                  "medicago"
+                  default: undefined
+-bssm             read bssm parameter from file in the path given by the
+                  environment variable BSSMDIR
+                  default: undefined
+-scorematrix      read amino acid substitution scoring matrix from file in the
+                  path given by the environment variable GTHDATADIR
+                  default: BLOSUM62
+-translationtable set the codon translation table used for codon translation in
+                  matching, DP, and output
+                  default: 1
+-f                analyze only forward strand of genomic sequences
+                  default: no
+-r                analyze only reverse strand of genomic sequences
+                  default: no
+-cdnaforward      align only forward strand of cDNAs
+                  default: no
+-frompos          analyze genomic sequence from this position
+                  requires -topos or -width; counting from 1 on
+                  default: 0
+-topos            analyze genomic sequence to this position
+                  requires -frompos; counting from 1 on
+                  default: 0
+-width            analyze only this width of genomic sequence
+                  requires -frompos
+                  default: 0
+-v                be verbose
+                  default: no
+-xmlout           show output in XML format
+                  default: no
+-gff3out          show output in GFF3 format
+                  default: no
+-md5ids           show MD5 fingerprints as sequence IDs
+                  default: no
+-o                redirect output to specified file
+                  default: undefined
+-gzip             write gzip compressed output file
+                  default: no
+-bzip2            write bzip2 compressed output file
+                  default: no
+-force            force writing to output file
+                  default: no
+-gs2out           output in old GeneSeqer2 format
+                  default: no
+-minmatchlen      specify minimum match length (cDNA matching)
+                  default: 20
+-seedlength       specify the seed length (cDNA matching)
+                  default: 18
+-exdrop           specify the Xdrop value for edit distance extension (cDNA
+                  matching)
+                  default: 2
+-prminmatchlen    specify minimum match length (protein matches)
+                  default: 24
+-prseedlength     specify seed length (protein matching)
+                  default: 10
+-prhdist          specify Hamming distance (protein matching)
+                  default: 4
+-gcmaxgapwidth    set the maximum gap width for global chains
+                  defines approximately the maximum intron length
+                  set to 0 to allow for unlimited length
+                  in order to avoid false-positive exons (lonely exons) at the
+                  sequence ends, it is very important to set this parameter
+                  appropriately!
+                  default: 1000000
+-gcmincoverage    set the minimum coverage of global chains regarding to the
+                  reference sequence
+                  default: 50
+-paralogs         compute paralogous genes (different chaining procedure)
+                  default: no
+-introncutout     enable the intron cutout technique
+                  default: no
+-fastdp           use jump table to increase speed of DP calculation
+                  default: no
+-autointroncutout set the automatic intron cutout matrix size in megabytes and
+                  enable the automatic intron cutout technique
+                  default: 0
+-intermediate     stop after calculation of spliced alignments and output
+                  results in reusable XML format. Do not process this output
+                  yourself, use the ``normal'' XML output instead!
+                  default: no
+-first            set the maximum number of spliced alignments per genomic DNA
+                  input. Set to 0 for unlimited number.
+                  default: 0
+-help             display help for basic options and exit
+-help+            display help for all options and exit
+-version          display version information and exit

debian/rules

@@ -10,6 +10,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 override_dh_clean:
 	dh_clean
 	rm -rf bin/bssm debian/bssm bin/gthdata debian/gthdata
+	rm -rf $(CURDIR)/debian/man
 
 override_dh_auto_build:
 	make licensemanager=no opt=yes 64bit=yes
@@ -26,7 +27,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 endif
 
 override_dh_installman:
-	#mkdir -p $(CURDIR)/debian/man
-	#asciidoctor -a docdate='' -b manpage $(CURDIR)/debian/man_src/*.adoc
-	#cp $(CURDIR)/debian/man_src/*.? $(CURDIR)/debian/man
+	mkdir -p $(CURDIR)/debian/man
+	asciidoctor -a docdate='' -b manpage $(CURDIR)/debian/man_src/*.adoc
+	cp $(CURDIR)/debian/man_src/*.? $(CURDIR)/debian/man
 	dh_installman --