debian/README.source

-multiqc for Debian
------------------
-
-Removing
-  .eggs folder since that is modified during build.
-
-and a series of files redundent with what is already in Debian, substituted
-with respective symbolic lincs
-  multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.ttf
-  multiqc/templates/default/assets/js/packages/jquery-3.1.1.min.js
-  multiqc/templates/default/assets/js/packages/jquery-ui.min.js
-  multiqc/templates/default/assets/js/packages/jquery.tablesorter.min.js
-  
-
-
- -- Steffen Moeller <moeller@debian.org>  Fri, 22 Mar 2019 18:40:49 +0100
-

debian/changelog

 multiqc (1.7+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #925304)
+  Non-free due to usage of Highcharts.  See
+      https://github.com/ewels/MultiQC/issues/800
 
  -- Andreas Tille <tille@debian.org>  Fri, 22 Mar 2019 08:07:09 +0100

debian/copyright

@@ -2,10 +2,7 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: MultiQC
 Source: https://github.com/ewels/MultiQC/
 Files-Excluded: .eggs
- multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.eot
- multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.ttf
- multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.woff
- multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.woff2
+ multiqc/templates/default/assets/fonts/glyphicons-halflings-regular.*
  multiqc/templates/default/assets/js/packages/jquery-3.1.1.min.js
  multiqc/templates/default/assets/js/packages/jquery-ui.min.js
  multiqc/templates/default/assets/js/packages/jquery.tablesorter.min.js
@@ -15,6 +12,11 @@ Files: *
 Copyright: 2015-2019 Phil Ewels <phil.ewels@scilifelab.se>
 License: GPL-3.0+
 
+Files: multiqc/templates/default/assets/js/packages/highcharts*
+Copyright: 2009-2016 Torstein Honsi
+License: Highcharts_non-free
+  http://www.highcharts.com/license
+
 Files: debian/*
 Copyright: 2019 Andreas Tille <tilla@debian.org>
                 Steffen Moeller <moeller@debian.org>

debian/createmanpages

+#!/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\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 \
+         --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

+debian/*.1

debian/multiqc-docs.docs

 README.Debian
-README.source

debian/multiqc.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH MULTIQC "1" "July 2019" "multiqc 1.7" "User Commands"
+.SH NAME
+multiqc \- output integration for RNA sequencing across tools and samples
+.SH SYNOPSIS
+.B multiqc
+[\fI\,OPTIONS\/\fR] \fI\,<analysis directory>\/\fR
+.SH DESCRIPTION
+MultiQC aggregates results from bioinformatics analyses across many
+samples into a single report.
+.P
+It searches a given directory for analysis logs and compiles a HTML
+report. It's a general use tool, perfect for summarising the output from
+numerous bioinformatics tools.
+.P
+To run, supply with one or more directory to scan for analysis results. To
+run here, use 'multiqc .'
+.SH OPTIONS
+.TP
+\fB\-f\fR, \fB\-\-force\fR
+Overwrite any existing reports
+.TP
+\fB\-d\fR, \fB\-\-dirs\fR
+Prepend directory to sample names
+.TP
+\fB\-dd\fR, \fB\-\-dirs\-depth\fR INTEGER
+Prepend [INT] directories to sample names.
+Negative number to take from start of path.
+.TP
+\fB\-s\fR, \fB\-\-fullnames\fR
+Do not clean the sample names (leave as full
+file name)
+.TP
+\fB\-i\fR, \fB\-\-title\fR TEXT
+Report title. Printed as page header, used
+for filename if not otherwise specified.
+.TP
+\fB\-b\fR, \fB\-\-comment\fR TEXT
+Custom comment, will be printed at the top
+of the report.
+.TP
+\fB\-n\fR, \fB\-\-filename\fR TEXT
+Report filename. Use 'stdout' to print to
+standard out.
+.TP
+\fB\-o\fR, \fB\-\-outdir\fR TEXT
+Create report in the specified output
+directory.
+.TP
+\fB\-t\fR, \fB\-\-template\fR [default|default_dev|geo|sections|simple]
+Report template to use.
+.TP
+\fB\-\-tag\fR TEXT
+Use only modules which tagged with this
+keyword, eg. RNA
+.TP
+\fB\-\-view\-tags\fR, \fB\-\-view_tags\fR
+View the available tags and which modules
+they load
+.TP
+\fB\-x\fR, \fB\-\-ignore\fR TEXT
+Ignore analysis files (glob expression)
+.TP
+\fB\-\-ignore\-samples\fR TEXT
+Ignore sample names (glob expression)
+.TP
+\fB\-\-ignore\-symlinks\fR
+Ignore symlinked directories and files
+.TP
+\fB\-\-sample\-names\fR PATH
+File containing alternative sample names
+.TP
+\fB\-l\fR, \fB\-\-file\-list\fR
+Supply a file containing a list of file
+paths to be searched, one per row
+.TP
+\fB\-e\fR, \fB\-\-exclude\fR [module name]
+Do not use this module. Can specify multiple
+times.
+.TP
+\fB\-m\fR, \fB\-\-module\fR [module name]
+Use only this module. Can specify multiple
+times.
+.TP
+\fB\-\-data\-dir\fR
+Force the parsed data directory to be
+created.
+.TP
+\fB\-\-no\-data\-dir\fR
+Prevent the parsed data directory from being
+created.
+.TP
+\fB\-k\fR, \fB\-\-data\-format\fR [tsv|json|yaml]
+Output parsed data in a different format.
+Default: tsv
+.TP
+\fB\-z\fR, \fB\-\-zip\-data\-dir\fR
+Compress the data directory.
+.TP
+\fB\-p\fR, \fB\-\-export\fR
+Export plots as static images in addition to
+the report
+.TP
+\fB\-fp\fR, \fB\-\-flat\fR
+Use only flat plots (static images)
+.TP
+\fB\-ip\fR, \fB\-\-interactive\fR
+Use only interactive plots (HighCharts
+Javascript)
+.TP
+\fB\-\-lint\fR
+Use strict linting (validation) to help code
+development
+.TP
+\fB\-\-pdf\fR
+Creates PDF report with 'simple' template.
+Requires Pandoc to be installed.
+.TP
+\fB\-\-no\-megaqc\-upload\fR
+Don't upload generated report to MegaQC,
+even if MegaQC options are found
+.TP
+\fB\-c\fR, \fB\-\-config\fR PATH
+Specific config file to load, after those in
+MultiQC dir / home dir / working dir.
+.TP
+\fB\-\-cl\-config\fR, \fB\-\-cl_config\fR TEXT
+Specify MultiQC config YAML on the command
+line
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Increase output verbosity.
+.TP
+\fB\-q\fR, \fB\-\-quiet\fR
+Only show log warnings
+.TP
+\fB\-\-version\fR
+Show the version and exit.
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Show this message and exit.
+.SH SEE ALSO
+See http://multiqc.info for more details.
+.SH AUTHOR
+Phil Ewels (http://phil.ewels.co.uk)
+.P
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/rules

@@ -5,20 +5,6 @@ export PYBUILD_NAME=multiqc
 # DH_VERBOSE := 1
 export LC_ALL=C.UTF-8
 
-include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-#                    specified by <https://reproducible-builds.org/specs/source-date-epoch/>
-
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
-
 %:
 	dh $@ --with python3 --buildsystem=pybuild