[med-svn] [scythe] 11/15: Add scythe man page

[Kevin Murray]

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

daube-guest pushed a commit to branch master
in repository scythe.

commit cbd252699d9c46e6128c37ad834e50191d6f3271
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Mon Apr 27 16:41:05 2015 +1000

    Add scythe man page
---
 debian/control         |  1 +
 debian/rules           |  4 ++++
 debian/scythe.1.ronn   | 39 +++++++++++++++++++++++++++++++++++++++
 debian/scythe.manpages |  1 +
 4 files changed, 45 insertions(+)

diff --git a/debian/control b/debian/control
index 2eb251f..8a0489c 100644
--- a/debian/control
+++ b/debian/control
@@ -5,6 +5,7 @@ Priority: optional
 Standards-Version: 3.9.6
 Build-Depends: debhelper (>= 9),
                zlib1g-dev,
+               ruby-ronn,
                check
 Homepage: https://github.com/vsbuffalo/scythe
 
diff --git a/debian/rules b/debian/rules
index 0d2168a..ae577d2 100755
--- a/debian/rules
+++ b/debian/rules
@@ -4,3 +4,7 @@ include /usr/share/dpkg/buildflags.mk
 
 %:
 	dh $@
+
+override_dh_auto_build:
+	dh_auto_build
+	ronn -r --manual=scythe --organization='Vince Buffalo' debian/scythe.1.ronn
diff --git a/debian/scythe.1.ronn b/debian/scythe.1.ronn
new file mode 100644
index 0000000..a0b03cc
--- /dev/null
+++ b/debian/scythe.1.ronn
@@ -0,0 +1,39 @@
+scythe(1) -- Bayesian adaptor trimmer
+=====================================
+
+
+## SYNOPSIS
+
+ scythe -t sanger -a /path/to/adaptors.fasta [options] <sequences.fastq.gz>
+
+
+ Trim 3'-end adapter contaminants off sequence files. If no output file
+ is specified, scythe will use stdout.
+
+## USAGE
+
+  -p, --prior		prior (default: 0.300)
+  -q, --quality-type	quality type, either illumina, solexa, or sanger (default: sanger)
+  -m, --matches-file	matches file (default: no output)
+  -o, --output-file	output trimmed sequences file (default: stdout)
+  -t, --tag		add a tag to the header indicating Scythe cut a sequence (default: off)
+  -n, --min-match	smallest contaminant to consider (default: 5)
+  -M, --min-keep	filter sequnces less than or equal to this length (default: 35)
+  --quiet		don't output statistics about trimming to stdout (default: off)
+  --help		display this help and exit
+  --version		output version information and exit
+
+  Information on quality schemes:
+  phred			PHRED quality scores (e.g. from Roche 454). ASCII with no offset, range: [4, 60].
+  sanger		Sanger are PHRED ASCII qualities with an offset of 33, range: [0, 93]. From
+			NCBI SRA, or Illumina pipeline 1.8+.
+  solexa		Solexa (also very early Illumina - pipeline < 1.3). ASCII offset of
+	 		64, range: [-5, 62]. Uses a different quality-to-probabilities conversion than other
+			schemes.
+  illumina		Illumina output from pipeline versions between 1.3 and 1.7. ASCII offset of 64,
+			range: [0, 62]
+
+## AUTHOR
+
+Vince Bufflo wrote scythe itself, while Kevin Murray made this man page and the
+Debian package
diff --git a/debian/scythe.manpages b/debian/scythe.manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/scythe.manpages
@@ -0,0 +1 @@
+debian/*.1

-- 
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