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commit f0b1efa94fc357e205eeb87955220fafaf580552 Author: Andreas Tille <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +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) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/manta.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
