[med-svn] r18041 - trunk/packages/prodigal/trunk/debian

[Andreas Tille]

Author: tille
Date: 2014-09-16 07:38:04 +0000 (Tue, 16 Sep 2014)
New Revision: 18041

Added:
   trunk/packages/prodigal/trunk/debian/createmanpages
   trunk/packages/prodigal/trunk/debian/prodigal.1
Modified:
   trunk/packages/prodigal/trunk/debian/changelog
   trunk/packages/prodigal/trunk/debian/control
   trunk/packages/prodigal/trunk/debian/prodigal.manpages
Log:
Use manually created manpage since help2man does a bad job


Modified: trunk/packages/prodigal/trunk/debian/changelog
===================================================================
--- trunk/packages/prodigal/trunk/debian/changelog	2014-09-16 07:30:10 UTC (rev 18040)
+++ trunk/packages/prodigal/trunk/debian/changelog	2014-09-16 07:38:04 UTC (rev 18041)
@@ -4,7 +4,7 @@
   * Add citation
   * `cme fix dpkg-control` to fix Vcs-Browser
   * Add myself as Uploader
-  * Build-Depends: help2man
+  * Use manually created manpage since help2man does a bad job
     Closes: #761684
   * d/watch: code moved to Github and changed versioning scheme
   * d/rules: override_dh_auto_install to prevent installing to /usr/local

Modified: trunk/packages/prodigal/trunk/debian/control
===================================================================
--- trunk/packages/prodigal/trunk/debian/control	2014-09-16 07:30:10 UTC (rev 18040)
+++ trunk/packages/prodigal/trunk/debian/control	2014-09-16 07:38:04 UTC (rev 18041)
@@ -4,8 +4,7 @@
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
-               help2man
+Build-Depends: debhelper (>= 9)
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/prodigal/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/prodigal/trunk/

Added: trunk/packages/prodigal/trunk/debian/createmanpages
===================================================================
--- trunk/packages/prodigal/trunk/debian/createmanpages	                        (rev 0)
+++ trunk/packages/prodigal/trunk/debian/createmanpages	2014-09-16 07:38:04 UTC (rev 18041)
@@ -0,0 +1,16 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name='microbial (bacterial and archaeal) gene finding program' \
+            --version-string="$VERSION" prodigal > $MANDIR/prodigal.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT
+


Property changes on: trunk/packages/prodigal/trunk/debian/createmanpages
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/prodigal/trunk/debian/prodigal.1
===================================================================
--- trunk/packages/prodigal/trunk/debian/prodigal.1	                        (rev 0)
+++ trunk/packages/prodigal/trunk/debian/prodigal.1	2014-09-16 07:38:04 UTC (rev 18041)
@@ -0,0 +1,62 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.2.
+.TH PRODIGAL "1" "September 2014" "prodigal 2.6.1" "User Commands"
+.SH NAME
+prodigal \- microbial (bacterial and archaeal) gene finding program
+.SH SYNOPSIS
+.B prodigal
+[\fI\,-a trans_file\/\fR] [\fI\,-c\/\fR] [\fI\,-d nuc_file\/\fR] [\fI\,-f output_type\/\fR]
+[\-g tr_table] [\-h] [\-i input_file] [\-m] [\-n] [\-o output_file]
+[\-p mode] [\-q] [\-s start_file] [\-t training_file] [\-v]
+.SH DESCRIPTION
+Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a
+microbial (bacterial and archaeal) gene finding program developed at
+Oak Ridge National Laboratory and the University of Tennessee.
+.SH OPTIONS
+.TP
+\fB\-a\fR:
+Write protein translations to the selected file.
+.TP
+\fB\-c\fR:
+Closed ends.  Do not allow genes to run off edges.
+.TP
+\fB\-d\fR:
+Write nucleotide sequences of genes to the selected file.
+.TP
+\fB\-f\fR:
+Select output format (gbk, gff, or sco).  Default is gbk.
+.TP
+\fB\-g\fR:
+Specify a translation table to use (default 11).
+.TP
+\fB\-h\fR:
+Print help menu and exit.
+.TP
+\fB\-i\fR:
+Specify input file (default reads from stdin).
+.TP
+\fB\-m\fR:
+Treat runs of n's as masked sequence and do not build genes across
+them.
+.TP
+\fB\-n\fR:
+Bypass the Shine\-Dalgarno trainer and force the program to scan
+for motifs.
+.TP
+\fB\-o\fR:
+Specify output file (default writes to stdout).
+.TP
+\fB\-p\fR:
+Select procedure (single or meta).  Default is single.
+.TP
+\fB\-q\fR:
+Run quietly (suppress normal stderr output).
+.TP
+\fB\-s\fR:
+Write all potential genes (with scores) to the selected file.
+.TP
+\fB\-t\fR:
+Write a training file (if none exists); otherwise, read and use
+the specified training file.
+.TP
+\fB\-v\fR:
+Print version number and exit.

Modified: trunk/packages/prodigal/trunk/debian/prodigal.manpages
===================================================================
--- trunk/packages/prodigal/trunk/debian/prodigal.manpages	2014-09-16 07:30:10 UTC (rev 18040)
+++ trunk/packages/prodigal/trunk/debian/prodigal.manpages	2014-09-16 07:38:04 UTC (rev 18041)
@@ -1 +1 @@
-prodigal.1
+debian/*.1