debian/IDeFIX.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
+.TH IDEFIX "1" "October 2019" "IDeFIX 1.3" "User Commands"
+.SH NAME
+IDeFIX \- index checking for improved demultiplexing of NGS data
+.SH SYNOPSIS
+.B IDeFIX
+[\-h] [\-j JOBS] [\-t THRESHOLD] [\-s SAMPLESHEET_NAME]
+[\-S SAMPLESHEET_OUTPUT] [\-c CORRECT_CHARS]
+[\-C ONLY_CHAR_CORRECT]
+projectpath
+.SH DESCRIPTION
+Index abundance report from Illumina NGS raw data and Sample Sheet correction
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+projectpath
+The path of the (top\-level) project folder.
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-j\fR JOBS, \fB\-\-jobs\fR JOBS
+Number of jobs/processes. (default: 20)
+.TP
+\fB\-t\fR THRESHOLD, \fB\-\-threshold\fR THRESHOLD
+Threshold for minimum number of reads of an index to
+be reported. (default: 1000)
+.TP
+\fB\-s\fR SAMPLESHEET_NAME, \fB\-\-samplesheet_name\fR SAMPLESHEET_NAME
+Defines the location of the Sample Sheet.
+.TP
+\fB\-S\fR SAMPLESHEET_OUTPUT, \fB\-\-samplesheet_output\fR SAMPLESHEET_OUTPUT
+Defines the location of the corrected SampleSheet.
+.TP
+\fB\-c\fR CORRECT_CHARS, \fB\-\-correct_chars\fR CORRECT_CHARS
+If True, removes backslashes, dots, tabs and
+whitespaces as well as umlauts from SampleSheet and
+saves the corrected version as SampleSheet.csv and the
+original as SampleSheet_beforeIDeFIX.csv. Subsequent
+actions are then performed with the corrected Sample
+Sheet (default: True)
+.TP
+\fB\-C\fR ONLY_CHAR_CORRECT, \fB\-\-only_char_correct\fR ONLY_CHAR_CORRECT
+Removal of undesired characters (backslashes, dots,
+tabs and whitespaces as well as umlauts) only.
+(default: False)
+.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

 idefix (1.3-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #<bug>)
+  TODO: python3-tz
 
  -- Andreas Tille <tille@debian.org>  Tue, 08 Oct 2019 08:25:37 +0200

debian/control

@@ -17,9 +17,12 @@ Architecture: any
 Depends: ${python3:Depends},
          ${misc:Depends},
          python3-numpy,
-         python3-pandas (>= 0.24.1),
-         python3-dateutil (>= 2.8.0),
-         python3-pytz (>= 2018.9),
+# FIXME: for the moment versioned Depends can not be fullfilled in Debian
+         python3-pandas,
+         python3-dateutil,
+#         python3-pandas (>= 0.24.1),
+#         python3-dateutil (>= 2.8.0),
+         python3-tz (>= 2018.9),
          python3-six (>= 1.12.0)
 Description: index checking for improved demultiplexing of NGS data
  IDeFIX is a tool for demultiplexing Illumina NGS data.

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\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=IDeFIX
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+         --name="$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/install

-IDeFIX*	usr/share/idefix
+IDeFIX.py	usr/share/idefix
+IDeFIX		usr/share/idefix
 

debian/links

-usr/share/idefix/IDeFIX.py	usr/bin/IDeFIX.py
+usr/share/idefix/IDeFIX.py	usr/bin/IDeFIX

debian/lintian-overrides

-# see https://lists.debian.org/debian-med/2018/06/msg00043.html
-idefix: script-with-language-extension usr/bin/*.*

debian/manpages

+debian/*.1

debian/rules

@@ -2,6 +2,8 @@
 
 # DH_VERBOSE := 1
 
+include /usr/share/dpkg/default.mk
+
 %:
 	dh $@ --with python3
 
@@ -11,3 +13,7 @@ override_dh_installdocs:
 	done
 	dh_installdocs
 	rm *.html
+
+override_dh_fixperms:
+	dh_fixperms
+	chmod -x debian/$(DEB_SOURCE)/usr/share/$(DEB_SOURCE)/*/*.py