[med-svn] [ruby-rgfa] 05/09: add manpages and tests

[Sascha Steinbiss]

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

satta pushed a commit to branch master
in repository ruby-rgfa.

commit aa11eeaab3bee629cefd729a1e6440969dc9396b
Author: Sascha Steinbiss <satta at debian.org>
Date:   Mon Sep 26 21:15:07 2016 +0000

    add manpages and tests
---
 debian/control                 |  7 ++++---
 debian/gfadiff.1.adoc          | 34 ++++++++++++++++++++++++++++++++++
 debian/manpages                |  1 +
 debian/rgfa-findcrisprs.1.adoc | 24 ++++++++++++++++++++++++
 debian/rgfa-mergelinear.1.adoc | 23 +++++++++++++++++++++++
 debian/rgfa-simdebruijn.1.adoc | 24 ++++++++++++++++++++++++
 debian/rules                   | 11 +++++++++++
 7 files changed, 121 insertions(+), 3 deletions(-)

diff --git a/debian/control b/debian/control
index 5e354f7..10869ec 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,9 @@ Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Sascha Steinbiss <satta at debian.org>
 Build-Depends: debhelper (>= 9~),
-               gem2deb
+               gem2deb,
+               rake,
+               asciidoctor
 Standards-Version: 3.9.8
 Vcs-Git: https://anonscm.debian.org/git/debian-med/ruby-rgfa.git
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ruby-rgfa.git
@@ -16,8 +18,7 @@ Package: ruby-rgfa
 Architecture: all
 XB-Ruby-Versions: ${ruby:Versions}
 Depends: ruby | ruby-interpreter,
-         ${misc:Depends},
-         ${shlibs:Depends}
+         ${misc:Depends}
 Description: parse, edit and write GFA format graphs in Ruby
  The Graphical Fragment Assembly (GFA) format is a proposed file format
  to describe the product of a genome sequence assembly process.
diff --git a/debian/gfadiff.1.adoc b/debian/gfadiff.1.adoc
new file mode 100644
index 0000000..8439bc1
--- /dev/null
+++ b/debian/gfadiff.1.adoc
@@ -0,0 +1,34 @@
+= gfadiff(1)
+:doctype: manpage
+
+== NAME
+
+gfadiff - compare two GFA files
+
+== SYNOPSIS
+
+*gfadiff* [-h] [-s] [-l] [-c] [-p] [-i] [-script] <gfa1> <gfa2>
+
+== DESCRIPTION
+
+If a combination of -h,-s,-l,-c and/or -p is specified, then
+only record of the specified type [h=headers, s=segments,
+l=links, c=containments, p=paths] are compared.
+(default: -h -s -l -c -p)
+
+== OTHER OPTIONS
+
+*-i*::
+  output message if identical
+
+*-script*::
+  create Ruby script to transform gfa1 into gfa2
+
+== SEE ALSO
+
+*rgfa-simdebruijn*(1), *rgfa-findcrispr*(1), *rgfa-mergelinear*(1)
+
+== BUGS
+
+Please report bugs to the RGFA issue tracker:
+https://github.com/ggonnella/rgfa/issues
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/rgfa-findcrisprs.1.adoc b/debian/rgfa-findcrisprs.1.adoc
new file mode 100644
index 0000000..9dfb5ca
--- /dev/null
+++ b/debian/rgfa-findcrisprs.1.adoc
@@ -0,0 +1,24 @@
+= rgfa-findcrisprs(1)
+:doctype: manpage
+
+== NAME
+
+rgfa-findcrisprs - find CRISPRs in assembly graphs
+
+== SYNOPSIS
+
+*rgfa-findcrisprs* <gfa>
+
+== DESCRIPTION
+
+Finds CRISPRs given in assembly graphs specified by a GFA file.
+CRISPRs have a structure ARU1RU..RUnRB where |U|~|R| in [24..50].
+
+== SEE ALSO
+
+*gfadiff*(1), *rgfa-mergelinear*(1), *rgfa-simdebruijn*(1)
+
+== BUGS
+
+Please report bugs to the RGFA issue tracker:
+https://github.com/ggonnella/rgfa/issues
diff --git a/debian/rgfa-mergelinear.1.adoc b/debian/rgfa-mergelinear.1.adoc
new file mode 100644
index 0000000..56764b7
--- /dev/null
+++ b/debian/rgfa-mergelinear.1.adoc
@@ -0,0 +1,23 @@
+= rgfa-mergelinear(1)
+:doctype: manpage
+
+== NAME
+
+rgfa-mergelinear - merge linear paths in assembly graphs
+
+== SYNOPSIS
+
+*rgfa-mergelinear* <gfa>
+
+== DESCRIPTION
+
+Merges linear paths in assembly graphs specified by a GFA file.
+
+== SEE ALSO
+
+*gfadiff*(1), *rgfa-findcrispr*(1), *rgfa-simdebruijn*(1)
+
+== BUGS
+
+Please report bugs to the RGFA issue tracker:
+https://github.com/ggonnella/rgfa/issues
diff --git a/debian/rgfa-simdebruijn.1.adoc b/debian/rgfa-simdebruijn.1.adoc
new file mode 100644
index 0000000..994bea3
--- /dev/null
+++ b/debian/rgfa-simdebruijn.1.adoc
@@ -0,0 +1,24 @@
+= rgfa-simdebruijn(1)
+:doctype: manpage
+
+== NAME
+
+rgfa-simdebruijn - simulate de Bruijn graphs
+
+== SYNOPSIS
+
+*rgfa-simdebruijn* <k> <genome.fas>
+
+== DESCRIPTION
+
+Outputs GFA format data simulating a de Bruijn graph on the input sequence
+<genome.fas> with k-mer size <k>.
+
+== SEE ALSO
+
+*gfadiff*(1), *rgfa-findcrispr*(1), *rgfa-mergelinear*(1)
+
+== BUGS
+
+Please report bugs to the RGFA issue tracker:
+https://github.com/ggonnella/rgfa/issues
diff --git a/debian/rules b/debian/rules
index 3454d59..38baabb 100755
--- a/debian/rules
+++ b/debian/rules
@@ -4,3 +4,14 @@ export GEM2DEB_TEST_RUNNER = --check-dependencies
 
 %:
 	dh $@ --buildsystem=ruby --with ruby
+
+override_dh_auto_clean:
+	rm -f debian/*.1
+	dh_auto_clean
+
+override_dh_auto_test:
+	rake test
+
+override_dh_installman:
+	asciidoctor -a docdate='' -b manpage debian/*.1.adoc
+	dh_installman

-- 
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