[med-svn] [manta] 02/02: Initial packaging

Andreas Tille tille at debian.org
Tue Nov 15 13:36:58 UTC 2016


This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository manta.

commit f0b1efa94fc357e205eeb87955220fafaf580552
Author: Andreas Tille <tille at debian.org>
Date:   Tue Nov 15 14:36:06 2016 +0100

    Initial packaging
---
 debian/changelog         |  6 ++++++
 debian/compat            |  1 +
 debian/control           | 44 ++++++++++++++++++++++++++++++++++++++++++++
 debian/copyright         | 27 +++++++++++++++++++++++++++
 debian/rules             | 28 ++++++++++++++++++++++++++++
 debian/source/format     |  1 +
 debian/upstream/metadata | 12 ++++++++++++
 debian/watch             |  4 ++++
 8 files changed, 123 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..81a0a54
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,6 @@
+manta (1.0.2+dfsg-1) UNRELEASED; urgency=medium
+
+  TODO: https://github.com/Illumina/pyflow
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Tue, 15 Nov 2016 14:29:08 +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..2d1a39f
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,44 @@
+Source: manta
+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),
+               cmake,
+               libboost-date-time-dev,
+               libboost-filesystem-dev,
+               libboost-program-options-dev,
+               libboost-regex-dev,
+               libboost-serialization-dev,
+               libboost-system-dev,
+               libboost-timer-dev,
+               libboost-chrono-dev,
+               libboost-test-dev,
+               zlib1g-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/manta.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/manta.git
+Homepage: https://github.com/Illumina/manta
+
+Package: manta
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: structural variant and indel caller for mapped sequencing data
+ Manta calls structural variants (SVs) and indels from mapped paired-end
+ sequencing reads. It is optimized for analysis of germline variation in
+ small sets of individuals and somatic variation in tumor/normal sample
+ pairs. Manta discovers, assembles and scores large-scale SVs, medium-
+ sized indels and large insertions within a single efficient workflow.
+ The method is designed for rapid analysis on standard compute hardware:
+ NA12878 at 50x genomic coverage is analyzed in less than 20 minutes on a
+ 20 core server, and most WGS tumor/normal analyses can be completed
+ within 2 hours. Manta combines paired and split-read evidence during SV
+ discovery and scoring to improve accuracy, but does not require split-
+ reads or successful breakpoint assemblies to report a variant in cases
+ where there is strong evidence otherwise. It provides scoring models for
+ germline variants in small sets of diploid samples and somatic variants
+ in matched tumor/normal sample pairs. There is experimental support for
+ analysis of unmatched tumor samples as well. Manta accepts input read
+ mappings from BAM or CRAM files and reports all SV and indel inferences
+ in VCF 4.1 format.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..9afd93d
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,27 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: manta
+Upstream-Contact: https://github.com/Illumina/manta/issues
+Source: https://github.com/Illumina/manta/releases
+Files-Excluded: redist/*.bz2
+
+Files: *
+Copyright: 2013-2016 Illumina, Inc.
+License: GPL-v3+
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: GPL-v3+
+
+License: GPL-v3+
+ This program 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 3 of the License, or
+ at your option) any later version.
+ .
+ This program 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.
+ .
+ On Debian systems you can find the full text of the GNU General Public
+ License at /usr/share/common-licenses/GPL-3.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..010ee79
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,28 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+# 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.
+
+# for hardening you might like to uncomment this:
+# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+CMAKE_EXTRA_FLAGS += -DCMAKE_BUILD_TYPE=Release
+
+%:
+	dh $@ --buildsystem=cmake
+
+override_dh_auto_configure:
+	dh_auto_configure -- $(CMAKE_EXTRA_FLAGS)
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..7252662
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: Xiaoyu Chen and Ole Schulz-Trieglaff and Richard Shaw and Bret Barnes and Felix Schlesinger and Morten Källberg and Anthony J. Cox and Semyon Kruglyak and Christopher T. Saunders
+  Title: "Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications"
+  Journal: Bioinformatics
+  Year: 2015
+  Volume: 32
+  Number: 8
+  Pages: 1220-1222
+  DOI: 10.1093/bioinformatics/btv710
+  PMID: 26647377
+  URL: http://bioinformatics.oxfordjournals.org/content/32/8/1220
+  eprint: http://bioinformatics.oxfordjournals.org/content/32/8/1220.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..ea65290
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=4
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+  https://github.com/Illumina/manta/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)

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