[med-svn] [nanook] 01/02: Fix pathes, add manpage
Andreas Tille
tille at debian.org
Fri Sep 1 13:59:17 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository nanook.
commit f659947dde27ed81e45b381abba7866a7a2e4b22
Author: Andreas Tille <tille at debian.org>
Date: Fri Sep 1 15:56:28 2017 +0200
Fix pathes, add manpage
---
debian/bin/nanook | 3 --
debian/createmanpages | 22 ++++++++
debian/install | 2 +-
debian/links | 1 +
debian/nanook.1 | 90 ++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
debian/patches/set_jar_path_in_bin.patch | 22 ++++++++
7 files changed, 137 insertions(+), 4 deletions(-)
diff --git a/debian/bin/nanook b/debian/bin/nanook
deleted file mode 100755
index fa9ba31..0000000
--- a/debian/bin/nanook
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/sh
-
-exec java -Xms128m -Xmx512m -jar /usr/share/java/nanook.jar "$@"
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..49a9951
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,22 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=nanook
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='flexible, multi-reference software for pre- and post-alignment analysis of nanopore sequencing data, quality and error profiles' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
diff --git a/debian/install b/debian/install
index 8e71dae..d997d3b 100644
--- a/debian/install
+++ b/debian/install
@@ -1 +1 @@
-debian/bin usr
+bin usr/share/nanook
diff --git a/debian/links b/debian/links
new file mode 100644
index 0000000..175907e
--- /dev/null
+++ b/debian/links
@@ -0,0 +1 @@
+usr/share/nanook/bin/nanook usr/bin/nanook
diff --git a/debian/nanook.1 b/debian/nanook.1
new file mode 100644
index 0000000..72c26ac
--- /dev/null
+++ b/debian/nanook.1
@@ -0,0 +1,90 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH NANOOK "1" "September 2017" "nanook 1.26" "User Commands"
+.SH NAME
+nanook \- flexible, multi-reference software for pre- and post-alignment analysis of nanopore sequencing data, quality and error profiles
+.SH SYNOPSIS
+.B nanook
+\fI<extract|align|analyse|compare|process>\fR [options]
+.SH DESCRIPTION
+ NanoOK (pronounced na-nook) is a tool for extraction, alignment and
+ analysis of Nanopore reads. NanoOK will extract reads as FASTA or FASTQ
+ files, align them (with a choice of alignment tools), then generate a
+ comprehensive multi-page PDF report containing yield, accuracy and
+ quality analysis. Along the way, it generates plain text files which can
+ be used for further analysis, as well as graphs suitable for inclusion
+ in presentations and papers.
+.SH OPTIONS
+.SS "extract options:"
+.HP
+\fB\-s\fR|\-sample <dir> specifies sample directory
+.HP
+\fB\-f\fR|\-reads specifies alternative dir for FAST5 files (default fast5)
+.IP
+Can be absolute (beginning with /) or relative
+e.g. \fB\-f\fR reads/downloads if replicating Metrichor file structure
+.HP
+\fB\-a\fR|\-fasta specifies FASTA file extraction (default)
+.HP
+\fB\-q\fR|\-fastq specifies FASTQ file extraction
+.HP
+\fB\-basecallindex\fR specifies the index of the analysis (default: latest)
+.HP
+\fB\-mergereads\fR to generate merged FASTA files in addition to single read files
+.HP
+\fB\-minquality\fR <value> to set the minimum quality for a 'pass' read
+.SS "align options:"
+.HP
+\fB\-s\fR|\-sample <dir> specifies sample directory
+.HP
+\fB\-r\fR|\-reference <path> specifies path to reference database
+.HP
+\fB\-aligner\fR <name> specifies the aligner (default last)
+.HP
+\fB\-alignerparams\fR <params> specifies paramters to the aligner
+.HP
+\fB\-showaligns\fR echoes aligner commands to screen
+.SS "analyse options:"
+.HP
+\fB\-s\fR|\-sample <dir> specifies sample directory
+.HP
+\fB\-r\fR|\-reference <path> specifies path to reference database
+.HP
+\fB\-aligner\fR <name> specifies the aligner (default last)
+.HP
+\fB\-coveragebin\fR <int> specifies coverage bin size (default 100)
+.HP
+\fB\-bitmaps\fR to output bitmap PNG graphs instead of PDF
+.SS "compare options:"
+.HP
+\fB\-l\fR|\-samplelist <file> specifies a sample list file
+.HP
+\fB\-o\fR|\-outputdir <directory> specifies an output directory
+.HP
+\fB\-type\fR <2d|template|complement> specifies an output directory
+.SS "process options:"
+.HP
+\fB\-process\fR <file> specifies a process file
+.SS "Read type options:"
+.HP
+\fB\-passonly\fR to analyse only pass reads
+.HP
+\fB\-failonly\fR to analyse only fail reads
+.HP
+\fB\-2donly\fR to analyse only 2D reads
+.HP
+\fB\-templateonly\fR to analyse just Template reads
+.HP
+\fB\-complementonly\fR to analyse just Complement reads
+.SS "Other options:"
+.HP
+\fB\-t\fR|\-numthreads <number> specifies the number of threads to use (default 1)
+.HP
+\fB\-log\fR <filename> enables debug logging to file
+.HP
+\fB\-force\fR to force NanoOK to ignore warnings
+.HP
+\fB\-timeout\fR to set the number of seconds before giving up waiting for new reads (default 2)
+.PP
+Valid aligners: last, bwa, blasr, marginalign, graphmap
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..91eadaa
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+set_jar_path_in_bin.patch
diff --git a/debian/patches/set_jar_path_in_bin.patch b/debian/patches/set_jar_path_in_bin.patch
new file mode 100644
index 0000000..fb36152
--- /dev/null
+++ b/debian/patches/set_jar_path_in_bin.patch
@@ -0,0 +1,22 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 01 Sep 2017 14:39:50 +0200
+Description: Set internal pathes to fit Debian package layout
+
+--- a/bin/nanook
++++ b/bin/nanook
+@@ -2,12 +2,14 @@
+
+ JAVA_ARGS="-Xmx2048m"
+
++export NANOOK_DIR=/usr/share/nanook
++
+ if [ -z "$NANOOK_DIR" ] ; then
+ echo "Error: You must set NANOOK_DIR before running."
+ exit 1
+ fi
+
+-JARFILE=${NANOOK_DIR}/dist/NanoOK.jar
++JARFILE=/usr/share/java/nanook.jar
+
+ if [ ! -f ${JARFILE} ] ; then
+ echo "Error: Can't find NanoOK.jar - it needs to be inside the dist subdirectory of the directory pointed to by NANOOK_DIR which is currently ${NANOOK_DIR}"
--
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