[med-svn] [Git][med-team/bio-rainbow][master] 4 commits: Add rudimentary manpages
Andreas Tille
gitlab at salsa.debian.org
Wed Jul 4 15:16:54 BST 2018
Andreas Tille pushed to branch master at Debian Med / bio-rainbow
Commits:
06adcdfa by Andreas Tille at 2018-07-04T15:41:28+02:00
Add rudimentary manpages
- - - - -
b2cdf22d by Andreas Tille at 2018-07-04T15:53:31+02:00
spelling, do not override dh_installman
- - - - -
3e3bb431 by Andreas Tille at 2018-07-04T16:12:32+02:00
Sort out some issues with manpages
- - - - -
6a9c7fa6 by Andreas Tille at 2018-07-04T16:13:36+02:00
Upload to unstable
- - - - -
14 changed files:
- − debian/bio-rainbow.manpages
- debian/changelog
- + debian/createmanpages
- + debian/manpages
- + debian/mans/bio-rainbow.1
- + debian/mans/ezmsim.1
- + debian/mans/rbasm.1
- + debian/mans/select_all_rbcontig.pl.1
- + debian/mans/select_best_rbcontig.pl.1
- + debian/mans/select_best_rbcontig_plus_read1.pl.1
- + debian/mans/select_sec_rbcontig.pl.1
- debian/patches/series
- + debian/patches/spelling.patch
- debian/rules
Changes:
=====================================
debian/bio-rainbow.manpages deleted
=====================================
--- a/debian/bio-rainbow.manpages
+++ /dev/null
@@ -1 +0,0 @@
-bio-rainbow.1
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-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 at debian.org> Wed, 04 Jul 2018 14:39:26 +0200
+ -- Andreas Tille <tille at debian.org> Wed, 04 Jul 2018 16:12:39 +0200
bio-rainbow (2.0.4-1) unstable; urgency=low
=====================================
debian/createmanpages
=====================================
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,63 @@
+#!/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
=====================================
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*.1
=====================================
debian/mans/bio-rainbow.1
=====================================
--- /dev/null
+++ b/debian/mans/bio-rainbow.1
@@ -0,0 +1,76 @@
+.\" 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 at gmail.com, chongzechen at 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
=====================================
--- /dev/null
+++ b/debian/mans/ezmsim.1
@@ -0,0 +1,18 @@
+.\" 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 at 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
=====================================
--- /dev/null
+++ b/debian/mans/rbasm.1
@@ -0,0 +1,27 @@
+.\" 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
=====================================
--- /dev/null
+++ b/debian/mans/select_all_rbcontig.pl.1
@@ -0,0 +1,11 @@
+.\" 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
=====================================
--- /dev/null
+++ b/debian/mans/select_best_rbcontig.pl.1
@@ -0,0 +1,11 @@
+.\" 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
=====================================
--- /dev/null
+++ b/debian/mans/select_best_rbcontig_plus_read1.pl.1
@@ -0,0 +1,11 @@
+.\" 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
=====================================
--- /dev/null
+++ b/debian/mans/select_sec_rbcontig.pl.1
@@ -0,0 +1,11 @@
+.\" 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
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
add_hardening.patch
rename_binary.patch
+spelling.patch
=====================================
debian/patches/spelling.patch
=====================================
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,38 @@
+Author: Andreas Tille <tille at 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
=====================================
--- a/debian/rules
+++ b/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
View it on GitLab: https://salsa.debian.org/med-team/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de
--
View it on GitLab: https://salsa.debian.org/med-team/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de
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