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commit f659947dde27ed81e45b381abba7866a7a2e4b22 Author: Andreas Tille <[email protected]> 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 <[email protected]> +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}" -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/nanook.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
