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commit 0242aada7f5e915c718f727286ed660eb76370d7 Author: Michael R. Crusoe <[email protected]> Date: Sat Jun 25 11:02:04 2016 -0700 initial Debianization --- debian/changelog | 5 ++++ debian/clean | 2 ++ debian/compat | 1 + debian/control | 34 ++++++++++++++++++++++++++++ debian/copyright | 27 ++++++++++++++++++++++ debian/genmanpages.py | 21 +++++++++++++++++ debian/manpages | 1 + debian/patches/no-py-ext | 13 +++++++++++ debian/patches/series | 1 + debian/rules | 59 ++++++++++++++++++++++++++++++++++++++++++++++++ debian/source/format | 1 + debian/upstream/metadata | 12 ++++++++++ debian/watch | 7 ++++++ 13 files changed, 184 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..6e13a11 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +cnvkit (0.7.11-1) UNRELEASED; urgency=medium + + * Initial release. (Closes: #828176) + + -- Michael R. Crusoe <[email protected]> Sat, 25 Jun 2016 10:57:17 -0700 diff --git a/debian/clean b/debian/clean new file mode 100644 index 0000000..991ead8 --- /dev/null +++ b/debian/clean @@ -0,0 +1,2 @@ +debian/*.1 +debian/*.include 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..e9a3996 --- /dev/null +++ b/debian/control @@ -0,0 +1,34 @@ +Source: cnvkit +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Michael R. Crusoe <[email protected]> +Build-Depends: debhelper (>= 9), + dh-python, + python-all, + python-setuptools, + python-pyfaidx, + help2man, + python-biopython, + python-pandas, + python-numpy, + python-pysam, + python-scipy, + python-matplotlib, + python-pyvcf, + r-cran-pscbs, + python-subprocess32 +Standards-Version: 3.9.8 +Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/cnvkit.git +Vcs-Git: https://anonscm.debian.org/debian-med/cnvkit.git +Homepage: http://cnvkit.readthedocs.org +X-Python-Version: >= 2.7 + +Package: cnvkit +Architecture: all +Depends: ${python:Depends}, ${misc:Depends} +Description: Copy number variant detection from targeted DNA sequencing + A command-line toolkit and Python library for detecting copy number variants + and alterations genome-wide from targeted DNA sequencing. It is designed for + use with hybrid capture, including both whole-exome and custom target panels, + and short-read sequencing platforms such as Illumina and Ion Torrent. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..919a84b --- /dev/null +++ b/debian/copyright @@ -0,0 +1,27 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: cnvkit +Source: https://github.com/etal/cnvkit + +Files: * +Copyright: © 2013-2017 Eric Talevich +License: Apache-2.0 + +Files: debian/* +Copyright: © 2016 Michael R. Crusoe <[email protected]> +License: Apache-2.0 + +License: Apache-2.0 + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + . + http://www.apache.org/licenses/LICENSE-2.0 + . + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. + . + On Debian systems, the full text of the Apache License, Version 2.0 can be + found in the file `/usr/share/common-licenses/Apache-2.0' diff --git a/debian/genmanpages.py b/debian/genmanpages.py new file mode 100755 index 0000000..9745403 --- /dev/null +++ b/debian/genmanpages.py @@ -0,0 +1,21 @@ +#!/usr/bin/python +from __future__ import print_function +from cnvlib import commands +import os +import sys +if os.name == 'posix' and sys.version_info[0] < 3: + import subprocess32 as subprocess +else: + import subprocess + +for subcommand in commands.AP_subparsers._get_subactions(): + name = subcommand.dest + description = subcommand.help + if name == 'version': + break + with open("debian/cnvkit-%s.man.include" % name, "w") as f: + print("[NAME]", file=f) + print("cnvkit_%s \- %s" % (name, description), file=f) + subprocess.check_call(['help2man', '--no-info', '--version-string=%s' + % sys.argv[1], '--include=debian/cnvkit-%s.man.include' % name, + '--output=debian/cnvkit-%s.1' % name, './cnvkit %s' % name]) diff --git a/debian/manpages b/debian/manpages new file mode 100644 index 0000000..0f65186 --- /dev/null +++ b/debian/manpages @@ -0,0 +1 @@ +debian/*.1 diff --git a/debian/patches/no-py-ext b/debian/patches/no-py-ext new file mode 100644 index 0000000..4d1f624 --- /dev/null +++ b/debian/patches/no-py-ext @@ -0,0 +1,13 @@ +Author: Michael R. Crusoe <[email protected]> +Description: Remove .py extensions as per Debian policy +--- cnvkit.orig/setup.py ++++ cnvkit/setup.py +@@ -41,7 +41,7 @@ + 'cnvlib.ngfrills', + 'cnvlib.segmentation', + ], +- scripts=[join(DIR, 'cnvkit.py')] + glob(join(DIR, 'scripts/*.py')), ++ scripts=[join(DIR, 'cnvkit')] + glob(join(DIR, 'scripts/*')), + classifiers=[ + "Development Status :: 4 - Beta", + "Environment :: Console", diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..263d233 --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +no-py-ext diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..c5d8ae2 --- /dev/null +++ b/debian/rules @@ -0,0 +1,59 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 +export LC_ALL=C.UTF-8 +export PYBUILD_NAME=cnvkit +# 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 + +%: + dh $@ --with python2 --buildsystem=pybuild + +override_dh_auto_build: + mv cnvkit.py cnvkit + mv scripts/genome2access.py ./ + cd scripts; for script in *.py; do mv $${script} \ + cnvkit-$${script%%.py}; done + dh_auto_build + cd scripts; for script in *; do mv $${script} $${script##cnvkit-}.py; \ + done + mv cnvkit cnvkit.py + mv genome2access.py scripts/ + +override_dh_auto_install: + mv cnvkit.py cnvkit + mv scripts/genome2access.py ./ + cd scripts; for script in *.py; do mv $${script} \ + cnvkit-$${script%%.py}; done + dh_auto_install + help2man --no-info --version-option=version \ + --name="a command-line toolkit for copy number analysis." \ + ./cnvkit > debian/cnvkit.1 + debian/genmanpages.py ${VERSION} + cd scripts; for script in *; do PYTHONPATH=../ help2man --no-info \ + --version-string=${VERSION} --help-option='-h' ./$${script} > \ + ../debian/$${script}.1; done + cd scripts; for script in *; do mv $${script} $${script##cnvkit-}.py; \ + done + mv cnvkit cnvkit.py + mv genome2access.py scripts/ + +override_dh_auto_test: + cd test; ${MAKE} + +override_dh_auto_clean: + cd test && ${MAKE} clean || /bin/true + dh_auto_clean 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..d8b5812 --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,12 @@ +Reference: + Author: + Title: + Journal: + Year: + Volume: + Number: + Pages: + DOI: + PMID: + URL: + eprint: diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..d14114e --- /dev/null +++ b/debian/watch @@ -0,0 +1,7 @@ +version=3 + +# Uncomment to find new files on Github +# - when using releases: +https://github.com/etal/cnvkit/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) +# if you need to repack and choose +dfsg prefix +# opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,compress=xz" \ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnvkit.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
