[med-svn] [scythe] 11/15: Add scythe man page
Kevin Murray
daube-guest at moszumanska.debian.org
Sun May 10 08:05:54 UTC 2015
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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