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}.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/kaptive.py.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
+.TH KAPTIVE.PY "1" "September 2019" "kaptive.py 0.6.0" "User Commands"
+.SH NAME
+kaptive.py \- obtain information about K and O types for Klebsiella genome assemblies
+.SH SYNOPSIS
+.B kaptive.py
+[\-h] [\-\-version] \fB\-a\fR ASSEMBLY [ASSEMBLY ...] \fB\-k\fR K_REFS
+[\-g ALLELIC_TYPING] [\-o OUT] [\-v] [\-t THREADS]
+[\-\-no_seq_out] [\-\-no_table] [\-\-no_json]
+[\-\-start_end_margin START_END_MARGIN]
+[\-\-min_gene_cov MIN_GENE_COV] [\-\-min_gene_id MIN_GENE_ID]
+[\-\-low_gene_id LOW_GENE_ID]
+[\-\-min_assembly_piece MIN_ASSEMBLY_PIECE]
+[\-\-gap_fill_size GAP_FILL_SIZE] [\-\-locus_label LOCUS_LABEL]
+.SH OPTIONS
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-version\fR
+Show Kaptive's version number and exit
+.TP
+\fB\-a\fR ASSEMBLY [ASSEMBLY ...], \fB\-\-assembly\fR ASSEMBLY [ASSEMBLY ...]
+FASTA file(s) for assemblies (default: None)
+.TP
+\fB\-k\fR K_REFS, \fB\-\-k_refs\fR K_REFS
+GenBank file with reference loci (default: None)
+.TP
+\fB\-g\fR ALLELIC_TYPING, \fB\-\-allelic_typing\fR ALLELIC_TYPING
+SRST2\-formatted FASTA file of allelic typing genes to
+include in results (default: None)
+.TP
+\fB\-o\fR OUT, \fB\-\-out\fR OUT
+Output directory/prefix (default: ./kaptive_results)
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Display detailed information about each assembly in
+stdout (default: False)
+.TP
+\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
+The number of threads to use for the BLAST searches
+(default: 4)
+.TP
+\fB\-\-no_seq_out\fR
+Suppress output files of sequences matching locus
+(default: False)
+.TP
+\fB\-\-no_table\fR
+Suppress output of tab\-delimited table (default:
+False)
+.TP
+\fB\-\-no_json\fR
+Suppress output of JSON file (default: False)
+.TP
+\fB\-\-start_end_margin\fR START_END_MARGIN
+Missing bases at the ends of locus allowed in a
+perfect match. (default: 10)
+.TP
+\fB\-\-min_gene_cov\fR MIN_GENE_COV
+minimum required % coverage for genes (default: 90.0)
+.TP
+\fB\-\-min_gene_id\fR MIN_GENE_ID
+minimum required % identity for genes (default: 80.0)
+.TP
+\fB\-\-low_gene_id\fR LOW_GENE_ID
+genes with a % identity below this value will be
+flagged as low identity (default: 95.0)
+.TP
+\fB\-\-min_assembly_piece\fR MIN_ASSEMBLY_PIECE
+minimum locus matching assembly piece to return
+(default: 100)
+.TP
+\fB\-\-gap_fill_size\fR GAP_FILL_SIZE
+when separate parts of the assembly are found within
+this distance, they will be merged (default: 100)
+.TP
+\fB\-\-locus_label\fR LOCUS_LABEL
+In the Genbank file, the source feature must have a
+note identifying the locus name, starting with this
+label followed by a colon (e.g. /note="K locus: K1")
+(default: automatically determined)
+.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/lintian-overrides

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

debian/manpages

+debian/*.1

debian/rules

 #!/usr/bin/make -f
 
-# 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_installman:
+	dh_installman --language=C