[med-svn] [ariba] 05/06: simplify manpage building

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository ariba.

commit be048e320e72a48f1577ac115c9443d82bd93fe0
Author: Sascha Steinbiss <satta at debian.org>
Date:   Thu Aug 4 13:09:49 2016 +0000

    simplify manpage building
---
 debian/ariba.1.adoc | 46 ++++++++++++++++++++++++++++++++++------------
 debian/changelog    |  1 +
 debian/rules        |  2 +-
 3 files changed, 36 insertions(+), 13 deletions(-)

diff --git a/debian/ariba.1.adoc b/debian/ariba.1.adoc
index 425220c..86ca8ab 100644
--- a/debian/ariba.1.adoc
+++ b/debian/ariba.1.adoc
@@ -6,22 +6,37 @@ ariba - Antibiotic Resistance Identification By Assembly
 
 ## SYNOPSIS
 
-*ariba* <task> [options]
+*ariba* <subtool> [options]
 
 ## DESCRIPTION
 
-*ariba* is the main executable for the **ARIBA** software. The actual
-functionality is provided by the subtools:
+*ariba* is the main executable for the **ARIBA** software, a
+tool that identifies antibiotic resistance genes by running
+local assemblies.
+
+In general, the input is a FASTA file of reference sequences
+(can be a mix of genes and noncoding sequences) and paired
+sequencing reads. ARIBA reports which of the reference sequence
+were found, plus detailed information on the quality of the
+assemblies and any variants between the sequencing reads and the
+reference sequences.
+
+The actual functionality is provided by the subtools listed below.
+
+### Subtools
 
 *getref*::
   download reference data
 
 *prepareref*::
-  prepare reference data for running the pipeline
+  prepare reference data for input to "run"
 
 *run*::
   run the ARIBA local assembly pipeline
 
+*refquery*::
+  get cluster or sequence info from prepareref output
+
 *reportfilter*::
   Filter report.tsv file
 
@@ -29,20 +44,27 @@ functionality is provided by the subtools:
   summarise multiple reports made by "run"
 
 *flag*::
-  translate the meaning of a flag output by the pipeline
+  translate the meaning of a flag
 
 *aln2meta*::
-  make metadata input to preparef, using multialignment and SNPs
+  converts multi-aln fasta and SNPs to metadata
 
 *test*::
-  run on small test dataset
+  run small built-in test dataset
 
 *version*::
-  print version and exit
+  get versions and exit
+
+### Subtool help
+
+You can run
+
+    ariba <subtool> --help
+
+to show more information about how to run each subtool.
 
-## SEE ALSO
+## BUGS
 
-All subtools of ARIBA have their own respective manpages:
+Please report bugs to the ARIBA issue tracker:
+https://github.com/sanger-pathogens/ariba/issues
 
-ariba-aln2meta(1), ariba-flag(1), ariba-getref(1), ariba-prepareref(1),
-ariba-reportfilter(1), ariba-run(1), ariba-summary(1), ariba-test(1)
diff --git a/debian/changelog b/debian/changelog
index 3008d3e..4b4c774 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,6 +4,7 @@ ariba (2.1.0+ds-1) unstable; urgency=medium
   * Adjust dependencies to new upstream requirements.
   * Drop patches applied by upstream or made obsolete.
   * Add bindnow hardening.
+  * Simplify manpage building.
   * Change architecture to any as ariba now builds native
     Python extensions.
   * Add shlibs:Depends for ariba binary package.
diff --git a/debian/rules b/debian/rules
index 14caa88..0b9559d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -16,7 +16,7 @@ override_dh_auto_clean:
 override_dh_installman:
 	mkdir -p $(mandir)
 	asciidoctor -a docdate='' -b manpage -o $(mandir)/ariba.1 $(debfolder)/ariba.1.adoc
-	PYTHONPATH=. scripts/ariba 2>&1 | tail -n +13 | head -n 12 | $(debfolder)/make_man
+	#PYTHONPATH=. scripts/ariba 2>&1 | tail -n +10 | head -n 14 | $(debfolder)/make_man
 	dh_installman --
 
 override_dh_auto_test:

-- 
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