[med-svn] [art-nextgen-simulation-tools] 02/03: Add initial packaging
Andreas Tille
tille at debian.org
Tue Feb 16 19:09:51 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository art-nextgen-simulation-tools.
commit 2da4bfa42a32f9cd62ad2cfd035e57f877d8c663
Author: Andreas Tille <tille at debian.org>
Date: Tue Feb 16 17:03:32 2016 +0100
Add initial packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 36 ++++++++++++++++++++++++++++++++++++
debian/copyright | 31 +++++++++++++++++++++++++++++++
debian/rules | 22 ++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 5 +++++
8 files changed, 113 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..1880d15
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+art-nextgen-simulation-tools (3.19.15+dfsg-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 16 Feb 2016 15:19:22 +0100
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..af112f2
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,36 @@
+Source: art-nextgen-simulation-tools
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ dh-autoreconf,
+ libgsl-dev
+Standards-Version: 3.9.7
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/art-nextgen-simulation-tools.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/art-nextgen-simulation-tools.git
+Homepage: http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
+
+Package: art-nextgen-simulation-tools
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: simulation tools to generate synthetic next-generation sequencing reads
+ ART is a set of simulation tools to generate synthetic next-generation
+ sequencing reads. ART simulates sequencing reads by mimicking real
+ sequencing process with empirical error models or quality profiles
+ summarized from large recalibrated sequencing data. ART can also
+ simulate reads using user own read error model or quality profiles. ART
+ supports simulation of single-end, paired-end/mate-pair reads of three
+ major commercial next-generation sequencing platforms: Illumina's
+ Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to
+ test or benchmark a variety of method or tools for next-generation
+ sequencing data analysis, including read alignment, de novo assembly,
+ SNP and structure variation discovery. ART was used as a primary tool
+ for the simulation study of the 1000 Genomes Project . ART is
+ implemented in C++ with optimized algorithms and is highly efficient in
+ read simulation. ART outputs reads in the FASTQ format, and alignments
+ in the ALN format. ART can also generate alignments in the SAM
+ alignment or UCSC BED file format. ART can be used together with genome
+ variants simulators (e.g. VarSim) for evaluating variant calling tools
+ or methods.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..562c789
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,31 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ART
+Upstream-Contact: Weichun Huang <whduke at gmail.com>
+Source: http://www.niehs.nih.gov/research/resources/assets/docs/artsrcchocolatecherrycake031915linuxtgz.tgz
+Files-Excluded: art_454
+ art_SOLiD
+ art_illumina
+ */*.o
+ */.dirstamp
+ */.deps
+ */autom4te.cache
+ Makefile
+ Makefile.in
+ INSTALL
+ compile
+ config.h
+ config.log
+ config.status
+ depcomp
+ install-sh
+ missing
+ stamp-h1
+
+Files: *
+Copyright: 2008-2015 Weichun Huang <whduke at gmail.com>
+ Gabor T. Marth <gabor.marth at bc.edu>
+License: to_be_clarified
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: probably_same_as_above
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..540d578
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+%:
+ dh $@ --with autoreconf
+
+#get-orig-source:
+# . debian/get-orig-source
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..77d6e24
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Weichun Huang and Leping Li and Jason R. Myers and Gabor T. Marth
+ Title: "ART: a next-generation sequencing read simulator"
+ Journal: Bioinformatics
+ Year: 2012
+ Volume: 28
+ Number: 4
+ Pages: 593-594
+ DOI: 10.1093/bioinformatics/btr708
+ PMID: 22199392
+ URL: https://bioinformatics.oxfordjournals.org/content/28/4/593.abstract
+ eprint: https://bioinformatics.oxfordjournals.org/content/28/4/593.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..913ccd9
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,5 @@
+version=3
+
+opts="uversionmangle=s/^(\d\d)(\d\d)(\d\d)$/$1.$2.$3/,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+ http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ .*/artsrc[a-z]*(\d+)linuxtgz\.tgz
+
--
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