[med-svn] [ariba] 04/06: add manpages

[Sascha Steinbiss]

This is an automated email from the git hooks/post-receive script.

sascha-guest pushed a commit to branch master
in repository ariba.

commit 8cb38711c036a61a871a45be74c1ee66e1cdc0e2
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Sat Dec 5 10:55:19 2015 +0000

    add manpages
---
 debian/ariba.manpages |  1 +
 debian/control        | 38 ++++++++++++++++++++++++++------------
 debian/make_man       | 12 ++++++++++++
 debian/rules          | 12 ++++++++++++
 4 files changed, 51 insertions(+), 12 deletions(-)

diff --git a/debian/ariba.manpages b/debian/ariba.manpages
new file mode 100644
index 0000000..d2c65e3
--- /dev/null
+++ b/debian/ariba.manpages
@@ -0,0 +1 @@
+debian/man/*
\ No newline at end of file
diff --git a/debian/control b/debian/control
index e5a8354..90bbb5d 100644
--- a/debian/control
+++ b/debian/control
@@ -3,26 +3,40 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
 Section: science
 Priority: optional
-Testsuite: autopkgtest
-Build-Depends: debhelper (>= 9), python3, python3-setuptools, python3-pymummer,
-               python3-pysam, python3-openpyxl, fastaq (>= 3.10.0),
-               python3-nose,  python3-lxml
+Build-Depends: debhelper (>= 9),
+               python3,
+               python3-setuptools,
+               python3-pymummer,
+               python3-pysam,
+               python3-openpyxl,
+               fastaq (>= 3.10.0),
+               python3-nose,
+               python3-lxml,
+               help2man
 Standards-Version: 3.9.6
-Homepage: https://github.com/sanger-pathogens/ariba
-Vcs-Git: git://anonscm.debian.org/debian-med/ariba.git
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ariba.git
+Vcs-Git: git://anonscm.debian.org/debian-med/ariba.git
+Homepage: https://github.com/sanger-pathogens/ariba
 
 Package: ariba
 Architecture: all
-Depends: ${misc:Depends}, ${python3:Depends}, bowtie2 (>= 2.1.0),
-         cd-hit (>= 4.6), samtools (>= 1.2),
-         mummer, velvet (>= 1.2.07), python3-pymummer, python3-pysam,
-         python3-openpyxl, fastaq (>= 3.10.0), python3-lxml
+Depends: ${misc:Depends},
+         ${python3:Depends},
+         bowtie2 (>= 2.1.0),
+         cd-hit,
+         samtools (>= 1.2),
+         bcftools (>= 1.2)
+         mummer,
+         velvet (>= 1.2.07),
+         python3-pymummer,
+         python3-pysam,
+         python3-openpyxl,
+         fastaq (>= 3.10.0),
+         python3-lxml
 Description: Antibiotic Resistance Identification By Assembly
  ARIBA is a tool that identifies antibiotic resistance genes by running local
  assemblies.
  The input is a FASTA file of reference genes and paired sequencing reads. ARIBA
  reports which of the reference genes were found, plus detailed information on
  the quality of the assemblies and any variants between the sequencing reads
- and the reference genes. bcftools (>= 1.2),
-
+ and the reference genes.
diff --git a/debian/make_man b/debian/make_man
new file mode 100755
index 0000000..e80eeca
--- /dev/null
+++ b/debian/make_man
@@ -0,0 +1,12 @@
+#!/usr/bin/perl
+
+my $v = `PYTHONPATH=. scripts/ariba version`;
+
+while(<>) {
+	chomp;
+	my ($name, $desc) = split(/\s{2,}/);
+	my $uname = uc($name);
+	`PYTHONPATH=. help2man -N -o ./debian/man/ariba-$name.1 -n '$desc' --version-string='$v' 'scripts/ariba $name'`;
+	`sed -i 's/.TH ARIBA /.TH ARIBA-$uname /' debian/man/ariba-$name.1`;
+	`sed -i 's/ariba $name/ariba_$name/' debian/man/ariba-$name.1`;
+}
\ No newline at end of file
diff --git a/debian/rules b/debian/rules
index 04fc69b..afb1b23 100755
--- a/debian/rules
+++ b/debian/rules
@@ -2,6 +2,18 @@
 
 export PYBUILD_NAME=ariba
 
+mandir := $(CURDIR)/debian/man
+debfolder := $(CURDIR)/debian
+
 %:
 	dh $@ --with python3 --buildsystem=pybuild
 
+override_dh_installman:
+	mkdir -p $(mandir)
+	PYTHONPATH=. help2man -N -o debian/man/ariba.1 \
+	  -n 'Antibiotic Resistance Identification by Assembly' \
+	  --no-discard-stderr \
+	  --version-string=`PYTHONPATH=. scripts/ariba version` scripts/ariba
+	sed -i 's/.SH DESCRIPTION/.SH DESCRIPTION\\n.nf/' $(mandir)/ariba.1
+	scripts/ariba 2>&1 | tail -n +13 | debian/make_man
+	dh_installman --
\ No newline at end of file

-- 
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