debian/SalmID.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH SALMID "1" "December 2018" "SalmID 0.1.23" "User Commands"
+.SH NAME
+SalmID \- rapid Kmer based Salmonella identifier from sequence data
+.SH SYNOPSIS
+.B SalmID
+[\-h] [\-v] [\-i your_fastqgz] [\-e file_extension] [\-d directory]
+[\-r percentage, coverage or taxonomy] [\-m quick or thorough]
+.SH DESCRIPTION
+SalmID enables rapid confirmation of Salmonella spp. and subspp. from
+sequence data.  This is done by checking taxonomic ID of single isolate
+samples.  Currently only IDs Salmonella species and subspecies, and
+some common contaminants (Listeria, Escherichia).
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-i\fR your_fastqgz, \fB\-\-input_file\fR your_fastqgz
+Single fastq.gz file input, include path to file if
+file is not in same directory
+.TP
+\fB\-e\fR file_extension, \fB\-\-extension\fR file_extension
+File extension, if specified without "\-\-input_dir",
+SalmID will attempt to ID all files with this
+extension in current directory, otherwise files in
+input directory
+.TP
+\fB\-d\fR directory, \fB\-\-input_dir\fR directory
+Directory which contains data for identification, when
+not specified files in current directory will be
+analyzed.
+.TP
+\fB\-r\fR percentage, coverage or taxonomy, \fB\-\-report\fR percentage, coverage or taxonomy
+Report either percentage ("percentage") of clade
+specific kmers recovered, average kmer\-coverage
+("cov"), or taxonomy (taxonomic species ID, plus
+observed mean k\-mer coverages and expected coverage).
+.TP
+\fB\-m\fR quick or thorough, \fB\-\-mode\fR quick or thorough
+Quick [quick] or thorough [thorough] mode
+.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/bin/SalmID

+#!/usr/bin/python3
+# This file was created via
+#   pip3 install dist/salmid*.whl
+# and found in ~/.local/bin
+
+# -*- coding: utf-8 -*-
+import re
+import sys
+
+from salmid.core import main
+
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

debian/control

@@ -3,17 +3,21 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~)
+Build-Depends: debhelper (>= 11~),
+               dh-python,
+               python3,
+               python3-setuptools
 Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/salmid
 Vcs-Git: https://salsa.debian.org/med-team/salmid.git
 Homepage: https://github.com/hcdenbakker/SalmID
 
 Package: salmid
-Architecture: any
-Depends: ${shlibs:Depends},
+Architecture: all
+Depends: ${python3:Depends},
          ${misc:Depends}
-Description: rapid confirmation of Salmonella spp. and subspp. from sequence data
- SalmID is a Rapid tool to check taxonomic ID of single isolate samples.
- Currently only IDs Salmonella species and subspecies, and some common
- contaminants (Listeria, Escherichia).
+Description: rapid Kmer based Salmonella identifier from sequence data
+ SalmID enables rapid confirmation of Salmonella spp. and subspp. from
+ sequence data.  This is done by checking taxonomic ID of single isolate
+ samples.  Currently only IDs Salmonella species and subspecies, and
+ some common contaminants (Listeria, Escherichia).

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

+debian/bin	usr

debian/manpages

+debian/*.1

debian/rules

@@ -3,29 +3,9 @@
 # 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 $@
-
-### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
-#override_dh_auto_test:
-#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-#	do_stuff_for_testing
-#endif
+	dh $@ --with python3 --buildsystem=pybuild
 
-### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script
-#get-orig-source:
-#	. debian/get-orig-source
+override_dh_install:
+	dh_install
+	find debian -name __pycache__ | xargs rm -rf