[med-svn] [wgsim] 01/07: Initial, incomplete wgsim package

Sun Jul 5 06:35:33 UTC 2015

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

commit c1b915a1e49288c752944d5814f1742c4b0576b1
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Sun Jul 5 16:22:47 2015 +1000

    Initial, incomplete wgsim package
---
 debian/changelog      |  5 +++++
 debian/compat         |  1 +
 debian/control        | 21 ++++++++++++++++++++
 debian/copyright      | 35 ++++++++++++++++++++++++++++++++++
 debian/rules          | 14 ++++++++++++++
 debian/wgsim.1        | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++
 debian/wgsim.install  |  1 +
 debian/wgsim.manpages |  1 +
 8 files changed, 131 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..da8b99e
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+wgsim (0.3.1-r13-1) unstable; urgency=low
+
+  * Initial release (Closes: #791395)
+
+ -- Kevin Murray <spam at kdmurray.id.au>  Sat, 04 Jul 2015 10:43:34 +1000
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..9e8dbeb
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,21 @@
+Source: wgsim
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Kevin Murray <spam at kdmurray.id.au>
+Build-Depends: debhelper (>= 9),
+               zlib1g-dev
+Standards-Version: 3.9.6
+Homepage: https://github.com/lh3/wgsim
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/wgsim.git
+Vcs-Git: git://anonscm.debian.org/debian-med/wgsim.git
+
+Package: wgsim
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: wgsim -- simulate sequencing reads from a reference genome.
+ Wgsim is a small tool for simulating sequence reads from a reference genome.
+ It is able to simulate diploid genomes with SNPs and insertion/deletion
+ (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing
+ errors. It does not generate INDEL sequencing errors, but this can be partly
+ compensated by simulating INDEL polymorphisms.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..e435c78
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,35 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Contact: Heng Li <lh3 at me.com>
+Upstream-Name: wgsim
+Source: https://github.com/lh3/wgsim
+
+Files: *
+Copyright: 2008 Genome Research Ltd (GRL).
+           2011 Heng Li <lh3 at live.co.uk>
+License: Expat
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+
+Files: debian/*
+Copyright: 2015 Kevin Murray <spam at kdmurray.id.au>
+License: GPL-3+
+
+License: GPL-3+
+ See `/usr/share/common-licenses/GPL-3'.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..4f2bea7
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,14 @@
+#!/usr/bin/make -f
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+%:
+	dh $@
+
+override_dh_auto_build:
+	dh_auto_build
+	cc -o wgsim -Wall -O3 -I. -lz -lm wgsim.c
+
+get-orig-source:
+	@echo "Downloading source from GitHub"
+	wget -O wgsim_0.3.1-r13.orig.tar.gz https://api.github.com/repos/lh3/wgsim/tarball/a12da3375ff3b51a5594d4b6fa35591173ecc229
diff --git a/debian/wgsim.1 b/debian/wgsim.1
new file mode 100644
index 0000000..186d296
--- /dev/null
+++ b/debian/wgsim.1
@@ -0,0 +1,53 @@
+.TH WGSIM: "1" "July 2015" "wgsim" "User Commands"
+.SH NAME
+wgsim \-\- Whole-genome sequencing read simulator
+.PP
+Version: 0.3.1\-r13
+.SH SYNOPSIS
+.B wgsim
+[\fI\,options\/\fR] \fI\,<in.ref.fa> <out.read1.fq> <out.read2.fq>\/\fR
+.PP
+<in.ref.fa> must be a fasta file containing a reference genome.
+.PP
+<out.read1.fq> and <out.read2.fq> are the first and second read output files.
+.SH OPTIONS
+.TP
+\fB\-e\fR FLOAT
+base error rate [0.000]
+.TP
+\fB\-d\fR INT
+outer distance between the two ends [500]
+.TP
+\fB\-s\fR INT
+standard deviation [50]
+.TP
+\fB\-N\fR INT
+number of read pairs [1000000]
+.TP
+\fB\-1\fR INT
+length of the first read [70]
+.TP
+\fB\-2\fR INT
+length of the second read [70]
+.TP
+\fB\-r\fR FLOAT
+rate of mutations [0.0010]
+.TP
+\fB\-R\fR FLOAT
+fraction of indels [0.15]
+.TP
+\fB\-X\fR FLOAT
+probability an indel is extended [0.30]
+.TP
+\fB\-S\fR INT
+seed for random generator [\-1]
+.TP
+\fB\-A\fR FLOAT
+disgard if the fraction of ambiguous bases higher than FLOAT [0.05]
+.TP
+\fB\-h\fR
+haplotype mode
+.TP
+Parameter defaults are given in square brackets.
+.SH AUTHOR
+Heng Li, https://github.com/lh3/wgsim
diff --git a/debian/wgsim.install b/debian/wgsim.install
new file mode 100644
index 0000000..8663424
--- /dev/null
+++ b/debian/wgsim.install
@@ -0,0 +1 @@
+wgsim usr/bin
diff --git a/debian/wgsim.manpages b/debian/wgsim.manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/wgsim.manpages
@@ -0,0 +1 @@
+debian/*.1

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/wgsim.git

