debian/README.test

+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by installing the package resfinder-example and
+running the provided test which can be found afterwards in the current dir:
+
+    sh run-unit-test
+
+in order to confirm its integrity.

debian/changelog

-resfinder (3.2-1) UNRELEASED; urgency=medium
+resfinder (3.2-1) unstable; urgency=medium
 
-  * Initial release (Closes: #<bug>)
+  * Initial release (Closes: #944789)
 
- -- Andreas Tille <tille@debian.org>  Thu, 07 Nov 2019 12:41:11 +0100
+ -- Andreas Tille <tille@debian.org>  Fri, 15 Nov 2019 13:33:04 +0100

debian/control

@@ -19,7 +19,7 @@ Depends: ${python3:Depends},
          python3-cgecore,
          python3-tabulate,
          ncbi-blast+-legacy
-Description: identifies acquired antimicrobial resistance genes
+Description: identify acquired antimicrobial resistance genes
  ResFinder identifies acquired antimicrobial resistance genes in total or
  partial sequenced isolates of bacteria.
  .
@@ -34,7 +34,7 @@ Package: resfinder-example
 Architecture: all
 Depends: ${misc:Depends},
 Recommends: resfinder
-Description: identifies acquired antimicrobial resistance genes (example data)
+Description: identify acquired antimicrobial resistance genes (example data)
  ResFinder identifies acquired antimicrobial resistance genes in total or
  partial sequenced isolates of bacteria.
  .

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

 test.fsa			usr/share/doc/resfinder/examples
+debian/tests/run-unit-test	usr/share/doc/resfinder

debian/resfinder.docs

+debian/README.test

debian/resfinder.py.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
+.TH RESFINDER.PY "1" "November 2019" "resfinder.py 3.2" "User Commands"
+.SH NAME
+resfinder.py \- identify acquired antimicrobial resistance genes
+.SH SYNOPSIS
+.B resfinder.py
+[\-h] \fB\-i\fR INPUTFILE [INPUTFILE ...] [\-o OUT_PATH]
+[\-tmp TMP_DIR] [\-mp METHOD_PATH] [\-p DB_PATH]
+[\-d DATABASES] [\-l MIN_COV] [\-t THRESHOLD]
+[\-ao ACQ_OVERLAP] [\-matrix] [\-x] [\-q]
+.SH OPTIONS
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-i\fR INPUTFILE [INPUTFILE ...], \fB\-\-inputfile\fR INPUTFILE [INPUTFILE ...]
+FASTA or FASTQ input files.
+.TP
+\fB\-o\fR OUT_PATH, \fB\-\-outputPath\fR OUT_PATH
+Path to blast output
+.TP
+\fB\-tmp\fR TMP_DIR, \fB\-\-tmp_dir\fR TMP_DIR
+Temporary directory for storage of the results from
+the external software.
+.TP
+\fB\-mp\fR METHOD_PATH, \fB\-\-methodPath\fR METHOD_PATH
+Path to method to use (kma or blastn)
+.TP
+\fB\-p\fR DB_PATH, \fB\-\-databasePath\fR DB_PATH
+Path to the databases
+.TP
+\fB\-d\fR DATABASES, \fB\-\-databases\fR DATABASES
+Databases chosen to search in \- if none are specified
+all are used
+.TP
+\fB\-l\fR MIN_COV, \fB\-\-min_cov\fR MIN_COV
+Minimum coverage
+.TP
+\fB\-t\fR THRESHOLD, \fB\-\-threshold\fR THRESHOLD
+Blast threshold for identity
+.TP
+\fB\-ao\fR ACQ_OVERLAP, \fB\-\-acq_overlap\fR ACQ_OVERLAP
+Genes are allowed to overlap this number of
+nucleotides. Default: 30.
+.TP
+\fB\-matrix\fR, \fB\-\-matrix\fR
+Gives the counts all all called bases at each position
+in each mapped template. Columns are: reference base,
+A count, C count, G count, T count, N count, \- count.
+.TP
+\fB\-x\fR, \fB\-\-extented_output\fR
+Give extented output with allignment files, template
+and query hits in fasta and a tab seperated file with
+gene profile results
+.HP
+\fB\-q\fR, \fB\-\-quiet\fR
+.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/rules

@@ -2,3 +2,6 @@
 
 %:
 	dh $@ --with python3
+
+override_dh_installman:
+	dh_installman --language=C