[med-svn] [ariba] 05/06: simplify manpage building
Sascha Steinbiss
satta at debian.org
Thu Aug 4 13:42:40 UTC 2016
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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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