[med-svn] [dwgsim] 02/03: Add initial debianising of dwgsim
Kevin Murray
daube-guest at moszumanska.debian.org
Wed Sep 23 01:01:45 UTC 2015
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a commit to branch master
in repository dwgsim.
commit f94391b2388eb4977fca07740ab0163571a14607
Author: Kevin Murray <spam at kdmurray.id.au>
Date: Wed Sep 23 10:09:00 2015 +1000
Add initial debianising of dwgsim
---
debian/changelog | 5 +++
debian/compat | 1 +
debian/control | 17 +++++++
debian/copyright | 62 ++++++++++++++++++++++++++
debian/dwgsim.1 | 119 +++++++++++++++++++++++++++++++++++++++++++++++++
debian/dwgsim.manpages | 1 +
debian/rules | 16 +++++++
debian/source/format | 1 +
debian/watch | 3 ++
9 files changed, 225 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..2d3ebda
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+dwgsim (0.1.11-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Kevin Murray <spam at kdmurray.id.au> Wed, 23 Sep 2015 09:14:48 +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..ef5e0ff
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,17 @@
+Source: dwgsim
+Section: science
+Priority: optional
+Maintainer: Kevin Murray <spam at kdmurray.id.au>
+Build-Depends: debhelper (>= 9),
+ zlib1g-dev
+Standards-Version: 3.9.6
+Homepage: https://github.com/nh13/DWGSIM/
+Vcs-Git: git://anonscm.debian.org/debian-med/dwgsim.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/dwgsim.git/
+
+Package: dwgsim
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: a short sequencing read simulator
+ DWGSIM simulates short sequencing reads from modern sequencing platforms.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..25e57b6
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,62 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: dwgsim
+Source: https://github.com/nh13/DWGSIM
+
+Files: *
+Copyright: 2008 Genome Research Ltd
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+Files: src/mut_vcf.c,
+ src/mut_bed.h,
+ src/mut.c,
+ src/mut_txt.c,
+ src/contigs.c,
+ src/dwgsim.c,
+ src/mut_input.c,
+ src/mut_input.h,
+ src/dwgsim_opt.c,
+ src/mut_txt.h,
+ src/mut_vcf.h,
+ src/mut_bed.c,
+ src/regions_bed.c
+Copyright: 2008 Genome Research Ltd
+License: Expat
+
+Files: debian/*
+Copyright: 2015 Kevin Murray <spam at kdmurray.id.au>
+License: Expat
+
+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.
diff --git a/debian/dwgsim.1 b/debian/dwgsim.1
new file mode 100644
index 0000000..8287d08
--- /dev/null
+++ b/debian/dwgsim.1
@@ -0,0 +1,119 @@
+.TH DWGSIM: "1" "September 2015" "dwgsim: 0.1.11" "User Commands"
+.SH NAME
+dwgsim: \- a short read simulator
+.SH SYNOPSIS
+.B dwgsim
+[\fI\,options\/\fR] \fI\,<in.ref.fa> <out.prefix>\/\fR
+.SH DESCRIPTION
+DWGSIM is a short read simulator which simulates reads from modern sequencing
+platforms.
+.SH OPTIONS
+.TP
+\fB\-e\fR FLOAT
+per base/color/flow error rate of the first read [from 0.020 to 0.020 by 0.000]
+.TP
+\fB\-E\fR FLOAT
+per base/color/flow error rate of the second read [from 0.020 to 0.020 by 0.000]
+.TP
+\fB\-i\fR
+use the inner distance instead of the outer distance for pairs [False]
+.TP
+\fB\-d\fR INT
+outer distance between the two ends for pairs [500]
+.TP
+\fB\-s\fR INT
+standard deviation of the distance for pairs [50.000]
+.TP
+\fB\-N\fR INT
+number of read pairs (\fB\-1\fR to disable) [\-1]
+.TP
+\fB\-C\fR FLOAT
+mean coverage across available positions (\fB\-1\fR to disable) [100.00]
+.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\-F\fR FLOAT
+frequency of given mutation to simulate low fequency somatic mutations [0.5000]
+NB: freqeuncy F refers to the first strand of mutation, therefore mutations
+on the second strand occour with a frequency of 1\-F
+.TP
+\fB\-R\fR FLOAT
+fraction of mutations that are indels [0.10]
+.TP
+\fB\-X\fR FLOAT
+probability an indel is extended [0.30]
+.TP
+\fB\-I\fR INT
+the minimum length indel [1]
+.TP
+\fB\-y\fR FLOAT
+probability of a random DNA read [0.05]
+.TP
+\fB\-n\fR INT
+maximum number of Ns allowed in a given read [0]
+.TP
+\fB\-c\fR INT
+generate reads for [0]:
+0: Illumina
+1: SOLiD
+2: Ion Torrent
+.TP
+\fB\-S\fR INT
+generate reads [0]:
+0: default (opposite strand for Illumina, same strand for SOLiD/Ion Torrent)
+1: same strand (mate pair)
+2: opposite strand (paired end)
+.TP
+\fB\-f\fR STRING
+the flow order for Ion Torrent data [(null)]
+.TP
+\fB\-B\fR
+use a per\-base error rate for Ion Torrent data [False]
+.TP
+\fB\-H\fR
+haploid mode [False]
+.TP
+\fB\-z\fR INT
+random seed (\fB\-1\fR uses the current time) [\-1]
+.TP
+\fB\-M\fR
+generate a mutations file only [False]
+.TP
+\fB\-m\fR FILE
+the mutations txt file to re\-create [not using]
+.TP
+\fB\-b\fR FILE
+the bed\-like file set of candidate mutations [(null)]
+.TP
+\fB\-v\fR FILE
+the vcf file set of candidate mutations (use pl tag for strand) [(null)]
+.TP
+\fB\-x\fR FILE
+the bed of regions to cover [not using]
+.TP
+\fB\-P\fR STRING
+a read prefix to prepend to each read name [not using]
+.TP
+\fB\-q\fR STRING
+a fixed base quality to apply (single character) [not using]
+.TP
+\fB\-Q\fR FLOAT
+standard deviation of the base quality scores [2.00]
+.TP
+\fB\-s\fR INT
+standard deviation of the distance for pairs [50.000]
+.TP
+\fB\-h\fR
+print this message
+.PP
+Note: For SOLiD mate pair reads and BFAST, the first read is F3 and the second is R3. For SOLiD mate pair reads
+and BWA, the reads in the first file are R3 the reads annotated as the first read etc.
+.PP
+Note: The longest supported insertion is 4294967295.
diff --git a/debian/dwgsim.manpages b/debian/dwgsim.manpages
new file mode 100644
index 0000000..662d78a
--- /dev/null
+++ b/debian/dwgsim.manpages
@@ -0,0 +1 @@
+debian/dwgsim.1
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..274f048
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,16 @@
+#!/usr/bin/make -f
+#export DH_VERBOSE = 1
+
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+
+# see ENVIRONMENT in dpkg-buildflags(1)
+# package maintainers to append CFLAGS
+#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
+# package maintainers to append LDFLAGS
+#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+
+
+%:
+ dh $@
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..317038c
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/nh13/DWGSIM/releases .*/archive/dwgsim\.?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
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