[med-svn] [Git][med-team/nanolyse][master] 2 commits: Upload to new

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / nanolyse


Commits:
4c14c038 by Andreas Tille at 2020-06-24T18:21:42+02:00
Upload to new

- - - - -
3b344b20 by Andreas Tille at 2020-06-24T18:26:28+02:00
Add manpage

- - - - -


4 changed files:

- + debian/NanoLyse.1
- debian/changelog
- + debian/createmanpages
- + debian/manpages


Changes:

=====================================
debian/NanoLyse.1
=====================================
@@ -0,0 +1,32 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
+.TH NANOLYSE "1" "June 2020" "NanoLyse 1.1.1" "User Commands"
+.SH NAME
+NanoLyse \- remove lambda phage reads from a fastq file
+.SH SYNOPSIS
+.B NanoLyse
+[\-h] [\-v] [\-r REFERENCE] [\-\-logfile LOGFILE]
+.SH DESCRIPTION
+Remove reads mapping to the lambda genome. Reads fastq from stdin and writes to stdout.
+.SH OPTIONS
+.SS "optional arguments:"
+.TP
+\fB\-r\fR, \fB\-\-reference\fR REFERENCE
+Specify a reference fasta file against which to filter.
+.TP
+\fB\-\-logfile\fR LOGFILE
+Specify the path and filename for the log file.
+.SS "General options:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show the help and exit
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+Print version and exit.
+.SH "EXAMPLES:"
+.IP
+gunzip \fB\-c\fR reads.fastq.gz | NanoLyse | gzip > reads_without_lambda.fastq.gz
+gunzip \fB\-c\fR reads.fastq.gz | NanoLyse | NanoFilt \fB\-q\fR 12 | gzip > filtered_reads_without_lambda.fastq.gz
+gunzip \fB\-c\fR reads.fastq.gz | NanoLyse \fB\-\-reference\fR mygenome.fa.gz | gzip > reads_without_mygenome.fastq.gz
+.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/changelog
=====================================
@@ -1,5 +1,5 @@
-nanolyse (1.1.1-1) UNRELEASED; urgency=medium
+nanolyse (1.1.1-1) unstable; urgency=medium
 
-  * Initial release (Closes: #<bug>)
+  * Initial release (Closes: #963620)
 
- -- Andreas Tille <tille at debian.org>  Fri, 15 May 2020 15:27:17 +0200
+ -- Andreas Tille <tille at debian.org>  Wed, 24 Jun 2020 18:21:30 +0200


=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,28 @@
+#!/bin/sh
+MANDIR=debian
+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: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=NanoLyse
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+         --name="$NAME" \
+            --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
=====================================
@@ -0,0 +1 @@
+debian/*.1



View it on GitLab: https://salsa.debian.org/med-team/nanolyse/-/compare/0c01ca756817f05bf1ce45b4f5c813020fbc0c92...3b344b2076a4ae34d651650e0754f79ffbc0546e

-- 
View it on GitLab: https://salsa.debian.org/med-team/nanolyse/-/compare/0c01ca756817f05bf1ce45b4f5c813020fbc0c92...3b344b2076a4ae34d651650e0754f79ffbc0546e
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