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commit 9f00fae0b31231119692bf01ae760c663cfc66ed Author: Steffen Moeller <[email protected]> Date: Sun Jan 15 08:41:40 2017 +0100 Initial release. --- debian/README.Debian | 11 ++++++++ debian/README.source | 10 +++++++ debian/changelog | 5 ++++ debian/compat | 1 + debian/control | 48 +++++++++++++++++++++++++++++++++ debian/copyright | 30 +++++++++++++++++++++ debian/patches/bd2k_as_short_name.patch | 13 +++++++++ debian/patches/series | 1 + debian/python-toil.postinst | 7 +++++ debian/python-toil.prerm | 15 +++++++++++ debian/rules | 32 ++++++++++++++++++++++ debian/source/format | 1 + debian/source/options | 1 + debian/toil-docs.docs | 2 ++ debian/watch | 15 +++++++++++ 15 files changed, 192 insertions(+) diff --git a/debian/README.Debian b/debian/README.Debian new file mode 100644 index 0000000..56fb748 --- /dev/null +++ b/debian/README.Debian @@ -0,0 +1,11 @@ +toil for Debian +--------------- + +This package is still preliminary since + * testing is not activated + * it is awkward to have both python2 and python3 supported, left it with python2 + * manpages are missing + * dependency on cgcloud https://github.com/BD2KGenomics/cgcloud not followed which ruins tests + +-- + Steffen Moeller <[email protected]> Sat, 14 Jan 2017 13:43:23 +0100 diff --git a/debian/README.source b/debian/README.source new file mode 100644 index 0000000..60d2966 --- /dev/null +++ b/debian/README.source @@ -0,0 +1,10 @@ +toil for Debian +--------------- + +The current version the package was derived from what was uploaded to the +pypi repository. This should be changed towards the gihub repository, +except for a lack of tags that are not set for the latest versions +available on Pypi. + + -- Steffen Moeller <[email protected]> Fri, 13 Jan 2017 15:58:18 +0100 + diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..54e1f97 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +toil (3.5.0~alpha1.321-1) unstable; urgency=medium + + * Initial release (Closes: #851365) + + -- Steffen Moeller <[email protected]> Fri, 13 Jan 2017 15:58:18 +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..8dba0aa --- /dev/null +++ b/debian/control @@ -0,0 +1,48 @@ +Source: toil +Section: net +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Steffen Moeller <[email protected]> +Build-Depends: debhelper (>= 9), dh-python, python-all, python-setuptools, python3-all, python3-setuptools +Standards-Version: 3.9.8 +Homepage: https://github.com/BD2KGenomics/toil +X-Python-Version: >= 2.6 +#X-Python3-Version: >= 3.2 +Vcs-Git: https://anonscm.debian.org/git/debian-med/toil.git +Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/toil.git +#Testsuite: autopkgtest-pkg-python + +Package: python-toil +Architecture: all +Depends: ${python:Depends}, ${misc:Depends}, python-cgcloud-lib +#Suggests: python-toil-doc +Conflicts: python3-toil +Description: cross-platform workflow engine (Python 2) + Toil is a scalable, efficient, cross-platform and easy-to-use workflow + engine in pure Python. It works with several well established load + balancers like Slurm or the Sun Grid Engine. Toil is compatible with + the Common Workflow Language (CWL). + . + This package installs the library for Python 2. + +#Package: python3-toil +#Architecture: all +#Depends: ${python3:Depends}, ${misc:Depends} +#Suggests: python-toil-doc +#Conflicts: python-toil +#Description: cross-platform workflow engine (Python 3) +# Toil is a scalable, efficient, cross-platform and easy-to-use workflow +# engine in pure Python. It works with several well established load +# balancers like Slurm or the Sun Grid Engine. Toil is compatible with +# the Common Workflow Language (CWL). +# . +# This package installs the library for Python 3. + +#Package: python-toil-doc +#Architecture: all +#Section: doc +#Depends: ${sphinxdoc:Depends}, ${misc:Depends} +#Description: cross-platform workflow engine (common documentation) +# The documentation of Toil shall go here at some point. +# . +# This is the common documentation package. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..dff32ca --- /dev/null +++ b/debian/copyright @@ -0,0 +1,30 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: toil +Source: https://github.com/BD2KGenomics/toil +Files-Excluded: src/toil.egg-info/* + +Files: * +Copyright: Benedict Paten <[email protected]> + 2015-2016 Regents of the University of California + 2015 UCSC Computational Genomics Lab +License: Apache-2.0 + +Files: debian/* +Copyright: 2017 Steffen Moeller <[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 + . + https://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 complete text of the Apache version 2.0 license + can be found in "/usr/share/common-licenses/Apache-2.0". diff --git a/debian/patches/bd2k_as_short_name.patch b/debian/patches/bd2k_as_short_name.patch new file mode 100644 index 0000000..e9caf35 --- /dev/null +++ b/debian/patches/bd2k_as_short_name.patch @@ -0,0 +1,13 @@ +Index: toil/setup.py +=================================================================== +--- toil.orig/setup.py ++++ toil/setup.py +@@ -30,7 +30,7 @@ def runSetup(): + author_email='[email protected]', + url="https://github.com/BD2KGenomics/toil";, + install_requires=[ +- 'bd2k-python-lib>=1.14a1.dev35', ++ 'bd2k>=1.14a1.dev35', + 'dill==0.2.5', + 'six>=1.10.0'], + extras_require={ diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..7aaeaf9 --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +bd2k_as_short_name.patch diff --git a/debian/python-toil.postinst b/debian/python-toil.postinst new file mode 100644 index 0000000..7b28cd4 --- /dev/null +++ b/debian/python-toil.postinst @@ -0,0 +1,7 @@ +#!/bin/sh +set -e + +update-alternatives --quiet --install /usr/bin/cwl-runner cwl-runner \ + /usr/bin/cwl-runner-toil 1 + +#DEBHELPER# diff --git a/debian/python-toil.prerm b/debian/python-toil.prerm new file mode 100644 index 0000000..d6c3c3c --- /dev/null +++ b/debian/python-toil.prerm @@ -0,0 +1,15 @@ +#!/bin/sh +set -e + +case "$1" in + remove) + update-alternatives --remove cwl-runner /usr/bin/cwl-runner-toil + ;; + + upgrade|failed-upgrade|deconfigure) + ;; + +esac + +#DEBHELPER# + diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..b3c7340 --- /dev/null +++ b/debian/rules @@ -0,0 +1,32 @@ +#!/usr/bin/make -f +# See debhelper(7) (uncomment to enable) +# output every command that modifies files on the build system. +#export DH_VERBOSE = 1 + +export PYBUILD_NAME=toil + +export PYBUILD_DESTDIR_python2=debian/python-toil/ +export PYBUILD_DESTDIR_python3=debian/python3-toil/ + +export PYBUILD_DISABLE=test +export PYBUILD_DISABLE_python3=1 + +%: + dh $@ --with python2 --buildsystem=pybuild + + +# If you need to rebuild the Sphinx documentation +# Add spinxdoc to the dh --with line +#override_dh_auto_build: +# dh_auto_build +# PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml docs/ build/html # HTML generator +# PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bman docs/ build/man # Manpage generator + +override_dh_auto_clean: + dh_auto_clean + rm -rf src/toil.egg-info + +override_dh_install: + dh_install + mv $(CURDIR)/debian/python-toil/usr/bin/cwl-runner $(CURDIR)/debian/python-toil/usr/bin/cwl-runner-toil + #mv $(CURDIR)/debian/python3-toil/usr/bin/cwl-runner $(CURDIR)/debian/python3-toil/usr/bin/cwl-runner-toil 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/source/options b/debian/source/options new file mode 100644 index 0000000..cb61fa5 --- /dev/null +++ b/debian/source/options @@ -0,0 +1 @@ +extend-diff-ignore = "^[^/]*[.]egg-info/" diff --git a/debian/toil-docs.docs b/debian/toil-docs.docs new file mode 100644 index 0000000..efea0a6 --- /dev/null +++ b/debian/toil-docs.docs @@ -0,0 +1,2 @@ +README.Debian +README.source diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..cf104b1 --- /dev/null +++ b/debian/watch @@ -0,0 +1,15 @@ +# Compulsory line, this is a version 4 file +version=4 + +# HTTP site (basic) +#http://example.com/downloads.html \ +# files/toil-([\d\.]+)\.tar\.gz debian uupdate + +# GitHub hosted projects +#opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%<project>-$1.tar.gz%" \ +# https://github.com/iBD2KGenomics/toil/tags \ +# (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate + +# PyPI +opts="uversionmangle=s%a(\d).dev(?)%~alpha$1.$2%" \ + https://pypi.debian.net/toil/toil-(.+)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/toil.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
