debian/bio-rainbow.manpages

-bio-rainbow.1

debian/changelog

-bio-rainbow (2.0.4+dfsg-1) UNRELEASED; urgency=medium
+bio-rainbow (2.0.4+dfsg-1) unstable; urgency=medium
 
   * Team upload.
 
@@ -17,8 +17,10 @@ bio-rainbow (2.0.4+dfsg-1) UNRELEASED; urgency=medium
   * DEP3
   * DEP5
   * hardening=+all
+  * Add rudimentary manpages
+  * spelling
 
- -- Andreas Tille <tille@debian.org>  Wed, 04 Jul 2018 14:39:26 +0200
+ -- Andreas Tille <tille@debian.org>  Wed, 04 Jul 2018 16:12:39 +0200
 
 bio-rainbow (2.0.4-1) unstable; urgency=low
 

debian/createmanpages

+#!/bin/sh
+MANDIR=debian/mans
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//'`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=ezmsim
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="simulate enzyme cut assembly sequences" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=rbasm
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+         --name="local assemble fragments around restriction sites" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=select_all_rbcontig.pl
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="select all rbcontig" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=select_best_rbcontig.pl
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="select best rbcontig" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=select_best_rbcontig_plus_read1.pl
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="select best rbcontig plus read1" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=select_sec_rbcontig.pl
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="select second rbcontig" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT

debian/manpages

+debian/mans/*.1

debian/mans/bio-rainbow.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH BIO-RAINBOW "1" "July 2018" "bio-rainbow 2.0.4" "User Commands"
+.SH NAME
+bio-rainbow \- clustering and assembling short reads for bioinformatics
+.SH SYNOPSIS
+.B rainbow
+\fI\,<cmd> \/\fR[\fI\,options\/\fR]
+.SH DESCRIPTION
+rainbow 2.0.4 \fB\-\-\fR <ruanjue@gmail.com, chongzechen@gmail.com>
+.IP
+cluster
+.PP
+Input  File Format: paired fasta/fastq file(s)
+Output File Format: <seqid:int>\et<cluster_id:int>\et<read1:string>\et<read2:string>
+.HP
+\fB\-1\fR <string> Input fasta/fastq file, supports multiple '\-1'
+.HP
+\fB\-2\fR <string> Input fasta/fastq file, supports multiple '\-2' [null]
+.TP
+\fB\-l\fR <int>
+Read length, default: 0 variable
+.TP
+\fB\-m\fR <int>
+Maximum mismatches [4]
+.TP
+\fB\-e\fR <int>
+Exactly matching threshold [2000]
+.TP
+\fB\-L\fR
+Low level of polymorphism
+.IP
+div
+.PP
+Input File Format: <seqid:int>\et<cluster_id:int>\et<read1:string>\et<read2:string>
+Output File Format: <seqid:int>\et<cluster_id:int>\et<read1:string>\et<read2:string>[\et<pre_cluster_id:int>]
+.HP
+\fB\-i\fR <string> Input file [stdin]
+.HP
+\fB\-o\fR <string> Output file [stdout]
+.TP
+\fB\-k\fR <int>
+K_allele, min variants to create a new group [2]
+.TP
+\fB\-K\fR <int>
+K_allele, divide regardless of frequency when num of variants exceed this value [50]
+.TP
+\fB\-f\fR <float>
+Frequency, min variant frequency to create a new group [0.2]
+.IP
+merge
+.PP
+Input File Format: <seqid:int>\et<cluster_id:int>\et<read1:string>\et<read2:string>[\et<pre_cluster_id:int>]
+.HP
+\fB\-i\fR <string> Input rbasm output file [stdin]
+.TP
+\fB\-a\fR
+output assembly
+.HP
+\fB\-o\fR <string> Output file for merged contigs, one line per cluster [stdout]
+.TP
+\fB\-N\fR <int>
+Maximum number of divided clusters to merge [300]
+.TP
+\fB\-l\fR <int>
+Minimum overlap when assemble two reads (valid only when '\-a' is opened) [5]
+.TP
+\fB\-f\fR <float>
+Minimum fraction of similarity when assembly (valid only when '\-a' is opened) [0.90]
+.TP
+\fB\-r\fR <int>
+Minimum number of reads to assemble (valid only when '\-a' is opened) [5]
+.TP
+\fB\-R\fR <int>
+Maximum number of reads to assemble (valid only when '\-a' is opened) [300]
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/ezmsim.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH EZMSIM "1" "July 2018" "ezmsim 2.0.4" "User Commands"
+.SH NAME
+ezmsim \- simulate enzyme cut assembly sequences
+.SH SYNOPSIS
+.B ezmsim
+\fI\,<LR|EF> \/\fR[\fI\,options\/\fR]
+.SH DESCRIPTION
+Program: ezmsim (simulate enzyme cut assembly sequences)
+Version: 0.1.1
+Contact: Zechen Chong <chongzechen@gmail.com>
+.PP
+Options: LR          simulate LR reads
+.TP
+RAD
+simulate RAD reads
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/rbasm.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH RBASM "1" "July 2018" "rbasm 2.0.4" "User Commands"
+.SH NAME
+rbasm \- local assemble fragments around restriction sites
+.SH SYNOPSIS
+.B ef
+[\fI\,options\/\fR]
+.SH DESCRIPTION
+Local assemble fragments around restriction sites
+.HP
+\fB\-i\fR <string> Input file [STDIN]
+.HP
+\fB\-o\fR <string> Output file [STDOUT]
+.TP
+\fB\-l\fR <int>
+Minimum length of overlap [5]
+.TP
+\fB\-s\fR <float>
+Minimum similiarity of overlap [0.90]
+.TP
+\fB\-r\fR <int>
+Minimum reads to execute assembly [5]
+.TP
+\fB\-R\fR <int>
+Maximum reads to execute assembly [200]
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/select_all_rbcontig.pl.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH SELECT_ALL_RBCONTIG.PL "1" "July 2018" "select_all_rbcontig.pl 2.0.4" "User Commands"
+.SH NAME
+select_all_rbcontig.pl \- select all rbcontig
+.SH SYNOPSIS
+.B select_all_rbcontig.pl
+\fI\,<rbasmed file>\/\fR
+.SH DESCRIPTION
+
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/select_best_rbcontig.pl.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH SELECT_BEST_RBCONTIG.PL "1" "July 2018" "select_best_rbcontig.pl 2.0.4" "User Commands"
+.SH NAME
+select_best_rbcontig.pl \- select best rbcontig
+.SH SYNOPSIS
+.B select_best_rbcontig.pl
+\fI\,<rbasmed file>\/\fR
+.SH DESCRIPTION
+
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/select_best_rbcontig_plus_read1.pl.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH SELECT_BEST_RBCONTIG_PLUS_READ1.PL "1" "July 2018" "select_best_rbcontig_plus_read1.pl 2.0.4" "User Commands"
+.SH NAME
+select_best_rbcontig_plus_read1.pl \- select best rbcontig plus read1
+.SH SYNOPSIS
+.B select_best_rbcontig_plus_read1.pl
+\fI\,<rbasmed file> <rbdiv output file>\/\fR
+.SH DESCRIPTION
+
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/select_sec_rbcontig.pl.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH SELECT_SEC_RBCONTIG.PL "1" "July 2018" "select_sec_rbcontig.pl 2.0.4" "User Commands"
+.SH NAME
+select_sec_rbcontig.pl \- select second rbcontig
+.SH SYNOPSIS
+.B select_sec_rbcontig.pl
+\fI\,<rbasmed file>\/\fR
+.SH DESCRIPTION
+
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/patches/series

 add_hardening.patch
 rename_binary.patch
+spelling.patch

debian/patches/spelling.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 04 Jul 2018 14:39:26 +0200
+Description: spelling
+
+--- a/README.txt
++++ b/README.txt
+@@ -93,10 +93,10 @@ NOTE: the input file format should be: <
+ Usage: rbasm [options]
+  -i <string> Input file [STDIN] 
+  -o <string> Output file [STDOUT]
+- -l <int>    Minium length of overlap [5]
+- -s <float>  Minium similiarity of overlap [0.90]
+- -r <int>    Minium reads to execute assembly [5]
+- -R <int>    Maxium reads to execute assembly [200]
++ -l <int>    Minimum length of overlap [5]
++ -s <float>  Minimum similiarity of overlap [0.90]
++ -r <int>    Minimum reads to execute assembly [5]
++ -R <int>    Maximum reads to execute assembly [200]
+ 
+ ----------------------------------------------------------------------------------
+ <Obsoleted> rbmergetag: a program merges divided results to evaluate clustering performance.
+--- a/asm_R2.c
++++ b/asm_R2.c
+@@ -397,10 +397,10 @@ int ef_usage(){
+ "Usage: ef [options]\n"
+ " -i <string> Input file [STDIN]\n"
+ " -o <string> Output file [STDOUT]\n"
+-" -l <int>    Minium length of overlap [5]\n"
+-" -s <float>  Minium similiarity of overlap [0.90]\n"
+-" -r <int>    Minium reads to execute assembly [5]\n"
+-" -R <int>    Maxium reads to execute assembly [200]\n"
++" -l <int>    Minimum length of overlap [5]\n"
++" -s <float>  Minimum similiarity of overlap [0.90]\n"
++" -r <int>    Minimum reads to execute assembly [5]\n"
++" -R <int>    Maximum reads to execute assembly [200]\n"
+ "\n"
+ 	);
+ 	return 1;

debian/rules

@@ -9,18 +9,9 @@ include /usr/share/dpkg/default.mk
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
-# see ENVIRONMENT in dpkg-buildflags(1)
-# package maintainers to append CFLAGS
-#export DEB_CFLAGS_MAINT_APPEND  = -Wall -pedantic
-# package maintainers to append LDFLAGS
-#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
-
-
-# main packaging script based on dh7 syntax
 %:
 	dh $@ 
 
 override_dh_installman:
-	help2man --no-discard-stderr  ./bio-rainbow > bio-rainbow.1
-	dh_installman
-
+	# dh_installman is messing up .sh extension as language extension
+	dh_install debian/mans/*.1 usr/share/man/man1