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commit c1b915a1e49288c752944d5814f1742c4b0576b1 Author: Kevin Murray <s...@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 <s...@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-packag...@lists.alioth.debian.org> +Uploaders: Kevin Murray <s...@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 <l...@me.com> +Upstream-Name: wgsim +Source: https://github.com/lh3/wgsim + +Files: * +Copyright: 2008 Genome Research Ltd (GRL). + 2011 Heng Li <l...@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 <s...@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 _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit