[med-svn] [Git][med-team/sniffles][master] 3 commits: Use dh_installman rather than debian/manpages
Afif Elghraoui pushed to branch master at Debian Med / sniffles Commits: e7f218e5 by Afif Elghraoui at 2018-07-08T00:44:17-04:00 Use dh_installman rather than debian/manpages The latter fails with `dpkg-buildpackage -B` because the file is apparently checked for existence before it is built. Closes: #903192 - - - - - b61ef3db by Afif Elghraoui at 2018-07-08T00:50:31-04:00 releasing package sniffles version 1.0.8+ds-2 - - - - - 025c00a6 by Afif Elghraoui at 2018-07-08T00:51:09-04:00 Merge branch master of ssh://salsa.debian.org/med-team/sniffles - - - - - 3 changed files: - debian/changelog - − debian/manpages - debian/rules Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +sniffles (1.0.8+ds-2) unstable; urgency=low + + * Use dh_installman rather than debian/manpages (Closes: #903192) + + -- Afif Elghraoui Sun, 08 Jul 2018 00:49:22 -0400 + sniffles (1.0.8+ds-1) unstable; urgency=medium * New upstream version = debian/manpages deleted = --- a/debian/manpages +++ /dev/null @@ -1 +0,0 @@ -debian/sniffles.1 = debian/rules = --- a/debian/rules +++ b/debian/rules @@ -28,7 +28,8 @@ override_dh_auto_test: bin/sniffles-*/sniffles -m test_set/reads_region.bam -v test.vcf ifeq ($(filter nodoc,$(DEB_BUILD_PROFILES)),) -build: debian/sniffles.1 +override_dh_installman: debian/sniffles.1 + dh_installman $^ else override_dh_installman: ; endif View it on GitLab: https://salsa.debian.org/med-team/sniffles/compare/d1bdb7fc6ed2b6fa8b3f743875c492665b940101...025c00a6981579342ecf92b9a14999ccbd8cc44a -- View it on GitLab: https://salsa.debian.org/med-team/sniffles/compare/d1bdb7fc6ed2b6fa8b3f743875c492665b940101...025c00a6981579342ecf92b9a14999ccbd8cc44a You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sniffles] Pushed new tag debian/1.0.8+ds-2
Afif Elghraoui pushed new tag debian/1.0.8+ds-2 at Debian Med / sniffles -- View it on GitLab: https://salsa.debian.org/med-team/sniffles/tree/debian/1.0.8+ds-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-gffutils][upstream] New upstream version 0.9
Steffen Möller pushed to branch upstream at Debian Med / python-gffutils Commits: 5d634a66 by Steffen Moeller at 2018-07-08T01:51:45+02:00 New upstream version 0.9 - - - - - 12 changed files: - PKG-INFO - README.rst - + doc/source/_templates/class.rst - gffutils.egg-info/PKG-INFO - gffutils.egg-info/SOURCES.txt - gffutils/constants.py - gffutils/convert.py - gffutils/create.py - gffutils/feature.py - gffutils/interface.py - gffutils/parser.py - gffutils/test/attr_test_cases.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/python-gffutils/commit/5d634a661165353809eec87f6497e15cf167a1e6 -- View it on GitLab: https://salsa.debian.org/med-team/python-gffutils/commit/5d634a661165353809eec87f6497e15cf167a1e6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-gffutils][pristine-tar] pristine-tar data for python-gffutils_0.9.orig.tar.gz
Steffen Möller pushed to branch pristine-tar at Debian Med / python-gffutils Commits: 867f0c99 by Steffen Moeller at 2018-07-08T01:51:52+02:00 pristine-tar data for python-gffutils_0.9.orig.tar.gz - - - - - 2 changed files: - + python-gffutils_0.9.orig.tar.gz.delta - + python-gffutils_0.9.orig.tar.gz.id Changes: = python-gffutils_0.9.orig.tar.gz.delta = Binary files /dev/null and b/python-gffutils_0.9.orig.tar.gz.delta differ = python-gffutils_0.9.orig.tar.gz.id = --- /dev/null +++ b/python-gffutils_0.9.orig.tar.gz.id @@ -0,0 +1 @@ +13d219e204e83d82cdc187d4c8154890c6d54bb4 View it on GitLab: https://salsa.debian.org/med-team/python-gffutils/commit/867f0c99f37c06f3feaf1afd74354f1a87db6714 -- View it on GitLab: https://salsa.debian.org/med-team/python-gffutils/commit/867f0c99f37c06f3feaf1afd74354f1a87db6714 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-gffutils][master] 2 commits: New upstream version 0.9
Steffen Möller pushed to branch master at Debian Med / python-gffutils Commits: 5d634a66 by Steffen Moeller at 2018-07-08T01:51:45+02:00 New upstream version 0.9 - - - - - b011e3a1 by Steffen Moeller at 2018-07-08T01:51:52+02:00 Update upstream source from tag upstream/0.9 Update to upstream version 0.9 with Debian dir 6a1b9c924050c0157633b5667aeba7cca0067945 - - - - - 0 changed files: Changes: View it on GitLab: https://salsa.debian.org/med-team/python-gffutils/compare/d75421eecef27a0079d2a7bea3b57748f18d8cf2...b011e3a1b85f46e9280f2b4f0679c3b1cc8a021c -- View it on GitLab: https://salsa.debian.org/med-team/python-gffutils/compare/d75421eecef27a0079d2a7bea3b57748f18d8cf2...b011e3a1b85f46e9280f2b4f0679c3b1cc8a021c You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-gffutils][master] Added packages for Python version 2
Steffen Möller pushed to branch master at Debian Med / python-gffutils
Commits:
d75421ee by Steffen Moeller at 2018-07-08T01:49:22+02:00
Added packages for Python version 2
Needed for bcbio.
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/rules
Changes:
=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -8,6 +8,8 @@ python-gffutils (0.9-1) UNRELEASED; urgency=medium
* d/u/metadata: Added RRIDs
+ * Added Python 2 packages, separated executable
+
-- Steffen Moeller Sun, 15 Apr 2018 14:03:00 +0200
python-gffutils (0.8.7.1-1) REMOVED; urgency=medium
=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,14 @@ Priority: optional
Build-Depends: debhelper (>= 10),
dh-python,
bedtools,
- python3,
+ python-all,
+ python-setuptools,
+ python-simplejson,
+ python-six,
+ python-pyfaidx,
+ python-nose,
+ python-biopython,
+ python-pybedtools,
python3-all,
python3-setuptools,
python3-simplejson,
@@ -17,11 +24,24 @@ Build-Depends: debhelper (>= 10),
python3-nose,
python3-biopython,
python3-pybedtools
-Standards-Version: 4.1.4
+Standards-Version: 4.1.3
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-gffutils.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/python-gffutils.git
Homepage: https://daler.github.io/gffutils
+Package: python-gffutils
+Architecture: all
+Depends: ${python2:Depends},
+ ${misc:Depends}
+Description: Work with GFF and GTF files in a flexible database framework
+ A Python package for working with and manipulating the GFF and GTF format
+ files typically used for genomic annotations. Files are loaded into a
+ sqlite3 database, allowing much more complex manipulation of hierarchical
+ features (e.g., genes, transcripts, and exons) than is possible with
+ plain-text methods alone.
+ .
+ This is the Python 2 version.
+
Package: python3-gffutils
Architecture: all
Depends: ${python3:Depends},
@@ -32,3 +52,29 @@ Description: Work with GFF and GTF files in a flexible
database framework
sqlite3 database, allowing much more complex manipulation of hierarchical
features (e.g., genes, transcripts, and exons) than is possible with
plain-text methods alone.
+ .
+ This is the Python 3 version.
+
+Package: python-gffutils-bin
+Architecture: all
+Depends: ${misc:Depends}, python-gffutils
+Description: Work with GFF and GTF files in a flexible database framework
+ A Python package for working with and manipulating the GFF and GTF format
+ files typically used for genomic annotations. Files are loaded into a
+ sqlite3 database, allowing much more complex manipulation of hierarchical
+ features (e.g., genes, transcripts, and exons) than is possible with
+ plain-text methods alone.
+ .
+ This package offers Python 2 executables.
+
+Package: python3-gffutils-bin
+Architecture: all
+Depends: ${misc:Depends}, python3-gffutils
+Description: Work with GFF and GTF files in a flexible database framework
+ A Python package for working with and manipulating the GFF and GTF format
+ files typically used for genomic annotations. Files are loaded into a
+ sqlite3 database, allowing much more complex manipulation of hierarchical
+ features (e.g., genes, transcripts, and exons) than is possible with
+ plain-text methods alone.
+ .
+ This package offers Python 3 executables.
=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -6,4 +6,13 @@ export PYBUILD_NAME=gffutils
export PYBUILD_DISABLE=test # https://github.com/daler/gffutils/issues/91
%:
- dh $@ --with python3 --buildsystem=pybuild
+ dh $@ --with python2,python3 --buildsystem=pybuild
+
+override_dh_auto_install:
+ dh_auto_install
+ mkdir -p debian/python-gffutils-bin/usr/bin
+ mkdir -p debian/python3-gffutils-bin/usr/bin
+ mv debian/python-gffutils/usr/bin/* debian/python-gffutils-bin/usr/bin/
+ mv debian/python3-gffutils/usr/bin/*
debian/python3-gffutils-bin/usr/bin/
+ rm -rf debian/python-gffutils/usr/bin debian/python3-gffutils/usr/bin
+
View it on GitLab:
https://salsa.debian.org/med-team/python-gffutils/commit/d75421eecef27a0079d2a7bea3b57748f18d8cf2
--
View it on GitLab:
https://salsa.debian.org/med-team/python-gffutils/commit/d75421eecef27a0079d2a7bea3b57748f18d8cf2
You're receiving this email because of your account on salsa.debian.org.
___
debian-med-commit mailing list
debian-med-com...@alioth-lists.debian.net
[med-svn] [Git][med-team/bcbio][upstream] New upstream version 1.0.9
Steffen Möller pushed to branch upstream at Debian Med / bcbio Commits: 6fe76bb3 by Steffen Möller at 2018-07-07T21:37:57+02:00 New upstream version 1.0.9 - - - - - 30 changed files: - .gitignore - .travis.yml - Dockerfile - HISTORY.md - README.rst - bcbio/bam/__init__.py - bcbio/bam/callable.py - bcbio/bam/trim.py - bcbio/broad/__init__.py - bcbio/chipseq/__init__.py - bcbio/chipseq/macs2.py - bcbio/chipseq/peaks.py - bcbio/cwl/create.py - bcbio/cwl/cwlutils.py - bcbio/cwl/defs.py - bcbio/cwl/tool.py - bcbio/cwl/workflow.py - bcbio/distributed/multitasks.py - bcbio/heterogeneity/__init__.py - bcbio/install.py - bcbio/ngsalign/alignprep.py - bcbio/ngsalign/postalign.py - bcbio/pipeline/alignment.py - bcbio/pipeline/cleanbam.py - bcbio/pipeline/datadict.py - bcbio/pipeline/genome.py - bcbio/pipeline/main.py - bcbio/pipeline/qcsummary.py - bcbio/pipeline/rnaseq.py - bcbio/pipeline/run_info.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/6fe76bb307966c27b636c92106df0df12bce2c49 -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/6fe76bb307966c27b636c92106df0df12bce2c49 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio][pristine-tar] pristine-tar data for bcbio_1.0.9.orig.tar.gz
Steffen Möller pushed to branch pristine-tar at Debian Med / bcbio Commits: 61ef8188 by Steffen Möller at 2018-07-07T21:38:32+02:00 pristine-tar data for bcbio_1.0.9.orig.tar.gz - - - - - 2 changed files: - + bcbio_1.0.9.orig.tar.gz.delta - + bcbio_1.0.9.orig.tar.gz.id Changes: = bcbio_1.0.9.orig.tar.gz.delta = Binary files /dev/null and b/bcbio_1.0.9.orig.tar.gz.delta differ = bcbio_1.0.9.orig.tar.gz.id = --- /dev/null +++ b/bcbio_1.0.9.orig.tar.gz.id @@ -0,0 +1 @@ +14486a8487128ea59864a198538a9e213c41ea58 View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/61ef81886d4b029da1c338ef2b6dc0aea1d465b2 -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/61ef81886d4b029da1c338ef2b6dc0aea1d465b2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio][master] 3 commits: Debian Med team maintenance
Andreas Tille pushed to branch master at Debian Med / bcbio
Commits:
da3f2fee by Andreas Tille at 2018-07-07T23:30:33+02:00
Debian Med team maintenance
- - - - -
4746ee6b by Andreas Tille at 2018-07-07T23:31:01+02:00
Drop ancient X-Python-Version* fields
- - - - -
77fd212e by Andreas Tille at 2018-07-08T00:10:39+02:00
cme fix dpkg-control
- - - - -
1 changed file:
- debian/control
Changes:
=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -1,29 +1,39 @@
Source: bcbio
+Maintainer: Debian Med Packaging Team
+Uploaders: Steffen Moeller
Section: science
+Testsuite: autopkgtest-pkg-python
Priority: optional
-Maintainer: Steffen Moeller
Build-Depends: debhelper (>= 10),
- dh-python, python-all, python-setuptools, python3-all, python3-setuptools,
- python3-toolz,
- python-logbook, python3-logbook,
- python-pysam, python3-pysam,
+ dh-python,
+ python-all,
+ python-setuptools,
+ python3-all,
+ python3-setuptools,
+ python3-toolz,
+ python-logbook,
+ python3-logbook,
+ python-pysam,
+ python3-pysam,
# python3-pybedtools,
- python3-gffutils,
- python-cyvcf2, python3-cyvcf2,
- python-pyvcf, python3-pyvcf,
- python-pandas, python3-pandas,
- python-mock, python3-mock
-Standards-Version: 4.1.3
-Homepage: https://github.com/chapmanb/bcbio-nextgen
-X-Python-Version: >= 2.6
-X-Python3-Version: >= 3.2
-Vcs-Git: https://salsa.debian.org/med-team/bcbio
+ python3-gffutils,
+ python-cyvcf2,
+ python3-cyvcf2,
+ python-pyvcf,
+ python3-pyvcf,
+ python-pandas,
+ python3-pandas,
+ python-mock,
+ python3-mock
+Standards-Version: 4.1.5
Vcs-Browser: https://salsa.debian.org/med-team/bcbio
-Testsuite: autopkgtest-pkg-python
+Vcs-Git: https://salsa.debian.org/med-team/bcbio.git
+Homepage: https://github.com/chapmanb/bcbio-nextgen
Package: python-bcbio
Architecture: all
-Depends: ${python:Depends}, ${misc:Depends}
+Depends: ${python:Depends},
+ ${misc:Depends}
#Suggests: python-bcbio-doc
Description: toolkit for analysing high-throughput sequencing data
This package installs the Python 2 libraries of the bcbio-nextgen
@@ -39,9 +49,10 @@ Description: toolkit for analysing high-throughput
sequencing data
Package: python3-bcbio
Architecture: all
-Depends: ${python3:Depends}, ${misc:Depends}
+Depends: ${python3:Depends},
+ ${misc:Depends}
#Suggests: python-bcbio-doc
-Description: toolkit for analysing high-throughput sequencing data
+Description: toolkit for analysing high-throughput sequencing data
This package installs the Python 3 libraries of the bcbio-nextgen
toolkit implementing best-practice pipelines for fully automated high
throughput sequencing analysis.
@@ -52,13 +63,3 @@ Description: toolkit for analysing high-throughput
sequencing data
contributes a shared community resource that handles the data processing
component of sequencing analysis, providing researchers with more time
to focus on the downstream biology.
-
-
-#Package: python-bcbio-doc
-#Architecture: all
-#Section: doc
-#Depends: ${sphinxdoc:Depends}, ${misc:Depends}
-#Description: (common documentation)
-#
-# .
-# This is the common documentation package.
View it on GitLab:
https://salsa.debian.org/med-team/bcbio/compare/419f6294364c6d147dfb2f7483030988b860e278...77fd212eba20763fb7116bc1f0b4c9a735f34490
--
View it on GitLab:
https://salsa.debian.org/med-team/bcbio/compare/419f6294364c6d147dfb2f7483030988b860e278...77fd212eba20763fb7116bc1f0b4c9a735f34490
You're receiving this email because of your account on salsa.debian.org.
___
debian-med-commit mailing list
debian-med-com...@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/autodock-vina][master] 6 commits: Remove Yask Gupta from Uploaders (thanks for your work Yask)
Andreas Tille pushed to branch master at Debian Med / autodock-vina Commits: 46db1988 by Andreas Tille at 2018-07-07T23:45:35+02:00 Remove Yask Gupta from Uploaders (thanks for your work Yask) - - - - - 41fc8f5d by Andreas Tille at 2018-07-07T23:46:49+02:00 debhelper 11 - - - - - 3e5e8c04 by Andreas Tille at 2018-07-07T23:54:37+02:00 DEP5 - - - - - 8878 by Andreas Tille at 2018-07-07T23:55:21+02:00 drop unneeded get-orig-source target - - - - - bdb72f86 by Andreas Tille at 2018-07-07T23:59:39+02:00 DEP3 - - - - - ce9204ac by Andreas Tille at 2018-07-08T00:08:14+02:00 Upload to unstable - - - - - 7 changed files: - debian/changelog - debian/compat - debian/control - debian/copyright - debian/patches/annoying_static_removed_was_in_for_a_reason_questionmark.patch - debian/patches/remove_static.patch - debian/rules Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -1,12 +1,20 @@ -autodock-vina (1.1.2-5) UNRELEASED; urgency=low +autodock-vina (1.1.2-5) unstable; urgency=low * Team upload. + + [ Liubov Chuprikova ] * Add autopkgtest Closes: #890785 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.5 * d/rules: add debug symbols and hardening + [ Andreas Tille ] + * Remove Yask Gupta from Uploaders (thanks for your work Yask) + * debhelper 11 + * DEP5 + * drop unneeded get-orig-source target + -- Liubov Chuprikova Sat, 07 Jul 2018 14:30:23 +0300 autodock-vina (1.1.2-4) unstable; urgency=low = debian/compat = --- a/debian/compat +++ b/debian/compat @@ -1 +1 @@ -10 +11 = debian/control = --- a/debian/control +++ b/debian/control @@ -1,12 +1,11 @@ Source: autodock-vina Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , - Yask Gupta , Michael Banck , Andreas Tille Section: science Priority: optional -Build-Depends: debhelper (>= 10), +Build-Depends: debhelper (>= 11~), libboost-all-dev Standards-Version: 4.1.5 Vcs-Browser: https://salsa.debian.org/med-team/autodock-vina = debian/copyright = --- a/debian/copyright +++ b/debian/copyright @@ -8,7 +8,21 @@ Files: * Copyright: © 2006-2011, The Scripps Research Institute Oleg Trott , Ruth Huey -License: Apache License, Version 2.0 +License: Apache-2.0 + +Files: debian/* +Copyright: © 2010 Yask Gupta + © 2010-2011 Steffen Moeller + © 2011 Andreas Tille +License: Apache-2.0 + +Files: debian/tests/test-data/* +Copyright: © 2018 Liubov Chuprikova +License: Apache-2.0 +Comment: Test data files were generated as it is discribed in Vina Video + Tutorial: http://vina.scripps.edu/tutorial.html + +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 @@ -23,17 +37,3 @@ License: Apache License, Version 2.0 . On Debian systems, the complete text of the Apache version 2.0 license can be found in `/usr/share/common-licenses/Apache-2.0'. - -Files: debian/* -Copyright: © 2010 Yask Gupta - © 2010-2011 Steffen Moeller - © 2011 Andreas Tille -License: Apache License, Version 2.0 - Same license as program itself. - -Files: debian/tests/test-data/* -Copyright: © 2018 Liubov Chuprikova -License: Apache License, Version 2.0 - Same license as program itself. -Comment: Test data files were generated as it is discribed in Vina Video - Tutorial: http://vina.scripps.edu/tutorial.html = debian/patches/annoying_static_removed_was_in_for_a_reason_questionmark.patch = --- a/debian/patches/annoying_static_removed_was_in_for_a_reason_questionmark.patch +++ b/debian/patches/annoying_static_removed_was_in_for_a_reason_questionmark.patch @@ -1,3 +1,6 @@ +Author: Steffen Moeller +Last-Update: 2011-05-12 11:02:35 + Index: autodock-vina-1.1.2/build/linux/debug/Makefile === --- autodock-vina-1.1.2.orig/build/linux/debug/Makefile2011-05-12 13:03:59.108034987 +0200 = debian/patches/remove_static.patch = --- a/debian/patches/remove_static.patch +++ b/debian/patches/remove_static.patch @@ -1,3 +1,6 @@ +Author: Steffen Moeller +Last-Update: 2011-05-12 11:02:35 + Index: autodock-vina-1.1.2/build/linux/release/Makefile === --- autodock-vina-1.1.2.orig/build/linux/release/Makefile 2011-05-12 15:45:29.468086887 +0200
[med-svn] [Git][med-team/autodock-vina] Pushed new tag debian/1.1.2-5
Andreas Tille pushed new tag debian/1.1.2-5 at Debian Med / autodock-vina -- View it on GitLab: https://salsa.debian.org/med-team/autodock-vina/tree/debian/1.1.2-5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bcbio][master] 5 commits: Preparing for 1.0.9 import
Steffen Möller pushed to branch master at Debian Med / bcbio Commits: f698b33e by Steffen Möller at 2018-07-07T21:37:38+02:00 Preparing for 1.0.9 import - - - - - 6fe76bb3 by Steffen Möller at 2018-07-07T21:37:57+02:00 New upstream version 1.0.9 - - - - - 8c77e243 by Steffen Möller at 2018-07-07T21:38:32+02:00 Update upstream source from tag upstream/1.0.9 Update to upstream version 1.0.9 with Debian dir dd5095e9059df6e9d1c66dfafb2ef37a990bee33 - - - - - f3321ce7 by Steffen Möller at 2018-07-07T23:18:46+02:00 Prepared for new 1.0.9 release. - - - - - 419f6294 by Steffen Möller at 2018-07-07T23:19:30+02:00 Merge branch master of salsa.debian.org:med-team/bcbio - - - - - 30 changed files: - .gitignore - .travis.yml - Dockerfile - HISTORY.md - README.rst - bcbio/bam/__init__.py - bcbio/bam/callable.py - bcbio/bam/trim.py - bcbio/broad/__init__.py - bcbio/chipseq/__init__.py - bcbio/chipseq/macs2.py - bcbio/chipseq/peaks.py - bcbio/cwl/create.py - bcbio/cwl/cwlutils.py - bcbio/cwl/defs.py - bcbio/cwl/tool.py - bcbio/cwl/workflow.py - bcbio/distributed/multitasks.py - bcbio/heterogeneity/__init__.py - bcbio/install.py - bcbio/ngsalign/alignprep.py - bcbio/ngsalign/postalign.py - bcbio/pipeline/alignment.py - bcbio/pipeline/cleanbam.py - bcbio/pipeline/datadict.py - bcbio/pipeline/genome.py - bcbio/pipeline/main.py - bcbio/pipeline/qcsummary.py - bcbio/pipeline/rnaseq.py - bcbio/pipeline/run_info.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/bcbio/compare/04fae2cc47566fc50fffd2f3a17dc7f8577f9725...419f6294364c6d147dfb2f7483030988b860e278 -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/compare/04fae2cc47566fc50fffd2f3a17dc7f8577f9725...419f6294364c6d147dfb2f7483030988b860e278 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/autodock-vina][master] d/rules: add debug symbols and hardening
Liubov Chuprikova pushed to branch master at Debian Med / autodock-vina Commits: b5f0817a by Liubov Chuprikova at 2018-07-07T16:50:00+03:00 d/rules: add debug symbols and hardening - - - - - 2 changed files: - debian/changelog - debian/rules Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -5,6 +5,7 @@ autodock-vina (1.1.2-5) UNRELEASED; urgency=low Closes: #890785 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.5 + * d/rules: add debug symbols and hardening -- Liubov Chuprikova Sat, 07 Jul 2018 14:30:23 +0300 = debian/rules = --- a/debian/rules +++ b/debian/rules @@ -5,10 +5,11 @@ # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 +export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow CFLAGS+=-fpermissive -DBOOST_FILESYSTEM_VERSION=3 --lto CXXFLAGS+=-fpermissive -DBOOST_FILESYSTEM_VERSION=3 --lto -LDFLAGS+=--lto +LDFLAGS+=--lto -g %: dh $@ View it on GitLab: https://salsa.debian.org/med-team/autodock-vina/commit/b5f0817a1a7a77ea11181b33bbbace451204229d -- View it on GitLab: https://salsa.debian.org/med-team/autodock-vina/commit/b5f0817a1a7a77ea11181b33bbbace451204229d You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/autodock-vina][master] Standards-Version: 4.1.5
Liubov Chuprikova pushed to branch master at Debian Med / autodock-vina Commits: 79b4d447 by Liubov Chuprikova at 2018-07-07T15:52:48+03:00 Standards-Version: 4.1.5 - - - - - 2 changed files: - debian/changelog - debian/control Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -4,6 +4,7 @@ autodock-vina (1.1.2-5) UNRELEASED; urgency=low * Add autopkgtest Closes: #890785 * Point Vcs fields to salsa.debian.org + * Standards-Version: 4.1.5 -- Liubov Chuprikova Sat, 07 Jul 2018 14:30:23 +0300 = debian/control = --- a/debian/control +++ b/debian/control @@ -8,7 +8,7 @@ Section: science Priority: optional Build-Depends: debhelper (>= 10), libboost-all-dev -Standards-Version: 4.1.0 +Standards-Version: 4.1.5 Vcs-Browser: https://salsa.debian.org/med-team/autodock-vina Vcs-Git: https://salsa.debian.org/med-team/autodock-vina.git Homepage: http://vina.scripps.edu View it on GitLab: https://salsa.debian.org/med-team/autodock-vina/commit/79b4d447af40d6bc65d56406195b2d298a95891a -- View it on GitLab: https://salsa.debian.org/med-team/autodock-vina/commit/79b4d447af40d6bc65d56406195b2d298a95891a You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/autodock-vina][master] Point Vcs fields to salsa.debian.org
Liubov Chuprikova pushed to branch master at Debian Med / autodock-vina Commits: c43a3e74 by Liubov Chuprikova at 2018-07-07T15:44:44+03:00 Point Vcs fields to salsa.debian.org - - - - - 2 changed files: - debian/changelog - debian/control Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -3,6 +3,7 @@ autodock-vina (1.1.2-5) UNRELEASED; urgency=low * Team upload. * Add autopkgtest Closes: #890785 + * Point Vcs fields to salsa.debian.org -- Liubov Chuprikova Sat, 07 Jul 2018 14:30:23 +0300 = debian/control = --- a/debian/control +++ b/debian/control @@ -9,8 +9,8 @@ Priority: optional Build-Depends: debhelper (>= 10), libboost-all-dev Standards-Version: 4.1.0 -Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/autodock-vina.git -Vcs-Git: https://anonscm.debian.org/git/debian-med/autodock-vina.git +Vcs-Browser: https://salsa.debian.org/med-team/autodock-vina +Vcs-Git: https://salsa.debian.org/med-team/autodock-vina.git Homepage: http://vina.scripps.edu Package: autodock-vina View it on GitLab: https://salsa.debian.org/med-team/autodock-vina/commit/c43a3e747ea16ef6a8ef7dc7f0962190f5ef5510 -- View it on GitLab: https://salsa.debian.org/med-team/autodock-vina/commit/c43a3e747ea16ef6a8ef7dc7f0962190f5ef5510 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/autodock-vina][master] Add autopkgtest
Liubov Chuprikova pushed to branch master at Debian Med / autodock-vina
Commits:
b99652e5 by Liubov Chuprikova at 2018-07-07T15:38:45+03:00
Add autopkgtest
- - - - -
9 changed files:
- + debian/README.test
- debian/changelog
- debian/copyright
- + debian/docs
- + debian/tests/control
- + debian/tests/run-unit-test
- + debian/tests/test-data/conf.txt
- + debian/tests/test-data/ligand.pdbqt
- + debian/tests/test-data/protein.pdbqt
Changes:
=
debian/README.test
=
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+___
+
+This package can be tested by execution
+
+ sh run-unit-test
+
+in order to confirm its integrity.
=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+autodock-vina (1.1.2-5) UNRELEASED; urgency=low
+
+ * Team upload.
+ * Add autopkgtest
+Closes: #890785
+
+ -- Liubov Chuprikova Sat, 07 Jul 2018 14:30:23 +0300
+
autodock-vina (1.1.2-4) unstable; urgency=low
[ Steffen Moeller ]
=
debian/copyright
=
--- a/debian/copyright
+++ b/debian/copyright
@@ -30,3 +30,10 @@ Copyright: © 2010 Yask Gupta
© 2011 Andreas Tille
License: Apache License, Version 2.0
Same license as program itself.
+
+Files: debian/tests/test-data/*
+Copyright: © 2018 Liubov Chuprikova
+License: Apache License, Version 2.0
+ Same license as program itself.
+Comment: Test data files were generated as it is discribed in Vina Video
+ Tutorial: http://vina.scripps.edu/tutorial.html
=
debian/docs
=
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+debian/tests/test-data
+debian/tests/run-unit-test
+debian/README.test
=
debian/tests/control
=
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,2 @@
+Tests: run-unit-test
+Depends: @
=
debian/tests/run-unit-test
=
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,20 @@
+#!/bin/sh -e
+
+pkg="autodock-vina"
+
+if [ "$AUTOPKGTEST_TMP" = "" ]; then
+AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XX)
+trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cd $AUTOPKGTEST_TMP
+cp /usr/share/doc/${pkg}/test-data/* .
+gunzip *.gz
+
+echo "Testing vina...\n"
+vina --config conf.txt --log log.txt
+
+echo "\nTesting vina_split...\n"
+vina_split --input out.pdbqt
+
+echo "\nPASS"
=
debian/tests/test-data/conf.txt
=
--- /dev/null
+++ b/debian/tests/test-data/conf.txt
@@ -0,0 +1,14 @@
+receptor = protein.pdbqt
+ligand = ligand.pdbqt
+
+out = out.pdbqt
+
+center_x = 11
+center_y = 90.5
+center_z = 57.5
+
+size_x = 22
+size_y = 24
+size_z = 28
+
+exhaustiveness = 4
=
debian/tests/test-data/ligand.pdbqt
=
--- /dev/null
+++ b/debian/tests/test-data/ligand.pdbqt
@@ -0,0 +1,66 @@
+REMARK 7 active torsions:
+REMARK status: ('A' for Active; 'I' for Inactive)
+REMARK1 Abetween atoms: C5_5 and C7_7
+REMARK2 Abetween atoms: C9_9 and N13_13
+REMARK3 Abetween atoms: N13_13 and C14_14
+REMARK4 Abetween atoms: C16_16 and N21_21
+REMARK Ibetween atoms: N21_21 and C22_22
+REMARK5 Abetween atoms: C22_22 and C23_23
+REMARK6 Abetween atoms: C27_26 and C46_30
+REMARK7 Abetween atoms: C46_30 and N48_31
+ROOT
+HETATM1 C1 STI 202 15.290 78.984 63.105 1.00 0.00-0.001 A
+HETATM2 C2 STI 202 14.162 78.322 62.514 1.00 0.00 0.095 A
+HETATM3 N3 STI 202 14.348 77.405 61.475 1.00 0.00-0.243 NA
+HETATM4 C4 STI 202 15.604 77.088 60.967 1.00 0.00 0.097 A
+HETATM5 C5 STI 202 16.790 77.718 61.516 1.00 0.00 0.020 A
+HETATM6 C6 STI 202 16.610 78.678 62.599 1.00 0.00 0.057 A
+ENDROOT
+BRANCH 5 7
+HETATM7 C7 STI 202 18.135 77.365 60.950 1.00 0.00 0.099 A
+HETATM8 N8 STI 202 18.991 76.649 61.763 1.00 0.00-0.061 NA
+HETATM9 C9 STI 202 20.233 76.272 61.350 1.00 0.00 0.728 A
+HETATM 10 N10 STI 202 20.667 76.608 60.078 1.00 0.00-0.059 NA
+HETATM 11 C11 STI 202 19.854 77.325 59.216 1.00 0.00 0.119 A
+HETATM 12 C12 STI 202 18.556 77.729 59.622 1.00 0.00 0.041 A
+BRANCH 9 13
+HETATM 13 N13 STI 202 21.026 75.546 62.243 1.00 0.00-0.190 N
+HETATM 14 H STI 202 20.822 74.493 62.382 1.00 0.00 0.184 HD
[med-svn] [Git][med-team/medicalterms] Pushed new tag debian/20160103-2
Andreas Tille pushed new tag debian/20160103-2 at Debian Med / medicalterms -- View it on GitLab: https://salsa.debian.org/med-team/medicalterms/tree/debian/20160103-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/medicalterms][master] 5 commits: Take over into Debian Med team maintenance
Andreas Tille pushed to branch master at Debian Med / medicalterms
Commits:
ba9d8b8d by Andreas Tille at 2018-07-07T09:12:49+02:00
Take over into Debian Med team maintenance
- - - - -
193423b5 by Andreas Tille at 2018-07-07T09:12:59+02:00
debhelper 11
- - - - -
3c3b8645 by Andreas Tille at 2018-07-07T14:44:04+02:00
Standards-Version: 4.1.5
- - - - -
72dc7a4a by Andreas Tille at 2018-07-07T14:44:33+02:00
Section: localization
- - - - -
64fec01c by Andreas Tille at 2018-07-07T14:45:33+02:00
Upload to unstable
- - - - -
3 changed files:
- debian/changelog
- debian/compat
- debian/control
Changes:
=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+medicalterms (20160103-2) unstable; urgency=medium
+
+ * Team upload.
+ * Take over into Debian Med team maintenance
+ * debhelper 11
+ * Standards-Version: 4.1.5
+ * Section: localization
+
+ -- Andreas Tille Sat, 07 Jul 2018 14:44:47 +0200
+
medicalterms (20160103-1) unstable; urgency=medium
* Imported Upstream version 20160103
=
debian/compat
=
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11
=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -1,15 +1,20 @@
Source: medicalterms
-Section: text
+Maintainer: Debian Med Packaging Team
+Uploaders: Dr. Tobias Quathamer
+Section: localization
Priority: optional
-Maintainer: Dr. Tobias Quathamer
-Build-Depends: debhelper (>= 9)
-Build-Depends-Indep: aspell-de, dictionaries-common-dev (>= 1.0)
-Standards-Version: 3.9.6
+Build-Depends: debhelper (>= 11~)
+Build-Depends-Indep: aspell-de,
+ dictionaries-common-dev
+Standards-Version: 4.1.5
+Vcs-Browser: https://salsa.debian.org/med-team/medicalterms
+Vcs-Git: https://salsa.debian.org/med-team/medicalterms.git
Homepage: https://github.com/toddy15/medicalterms
Package: wgerman-medical
Architecture: all
-Depends: ${misc:Depends}, dictionaries-common
+Depends: ${misc:Depends},
+ dictionaries-common
Provides: wordlist
Description: German medical dictionary words for /usr/share/dict
This package provides the file /usr/share/dict/german-medical containing
@@ -18,8 +23,9 @@ Description: German medical dictionary words for
/usr/share/dict
Package: hunspell-de-med
Architecture: all
-Depends: ${misc:Depends}, dictionaries-common,
- hunspell-de-de | hunspell-de-at | hunspell-de-ch
+Depends: ${misc:Depends},
+ dictionaries-common,
+ hunspell-de-de | hunspell-de-at | hunspell-de-ch
Description: German medical dictionary for hunspell
This package contains a German medical dictionary for use with the
hunspell spellchecker which is currently used within OpenOffice.org2
View it on GitLab:
https://salsa.debian.org/med-team/medicalterms/compare/4d1206190c565f0058c502043c4972fe8fda07b2...64fec01cb41fee2188013dec7889ac079c795010
--
View it on GitLab:
https://salsa.debian.org/med-team/medicalterms/compare/4d1206190c565f0058c502043c4972fe8fda07b2...64fec01cb41fee2188013dec7889ac079c795010
You're receiving this email because of your account on salsa.debian.org.
___
debian-med-commit mailing list
debian-med-com...@alioth-lists.debian.net
https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/medicalterms][master] 2 commits: Import Upstream version 20160103
Andreas Tille pushed to branch master at Debian Med / medicalterms Commits: 1981549b by Andreas Tille at 2018-07-07T08:39:32+02:00 Import Upstream version 20160103 - - - - - 4d120619 by Dr. Tobias Quathamer at 2018-07-07T08:39:32+02:00 Import Debian changes 20160103-1 medicalterms (20160103-1) unstable; urgency=medium * Imported Upstream version 20160103 - Make build reproducible. Closes: #793813 * Use debhelper v9 * Update homepage * Update watch file * Switch copyright to machine-readable format * Update to Standards-Version 3.9.6, no changes needed - - - - - 30 changed files: - + .gitignore - AUTHORS - ChangeLog - Makefile.am - Makefile.in - + README-medicalterms.md - README → README.md - aclocal.m4 - bin/Makefile.am - bin/Makefile.in - bin/convert_to_igerman98 - bin/find_dups - bin/get_words - bin/sort_file - configure - configure.ac - debian/changelog - debian/compat - debian/control - debian/copyright - debian/hunspell-de-med.docs - debian/watch - debian/wgerman-medical.docs - dicts/Makefile.am - dicts/Makefile.in - dicts/abkuerzungen-x-de_all-medicalterms.txt - dicts/adjektive-de_all-medicalterms.txt - dicts/ergaenzungen-xx-de_all-medicalterms.txt - dicts/medizin-a-de_all-medicalterms.txt - dicts/medizin-n-de_all-medicalterms.txt The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/medicalterms/compare/394a8b148fbf99bd941b4f598f4f6fd3a56d3fa1...4d1206190c565f0058c502043c4972fe8fda07b2 -- View it on GitLab: https://salsa.debian.org/med-team/medicalterms/compare/394a8b148fbf99bd941b4f598f4f6fd3a56d3fa1...4d1206190c565f0058c502043c4972fe8fda07b2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
