This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository roary.
commit b27d0a61c5f1dce951c135231544b9d67f1d754b Author: Sascha Steinbiss <[email protected]> Date: Thu Dec 17 22:56:27 2015 +0000 add debian dir --- debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 54 ++++++++++++++++++++++++++++++++++++++++++++++++ debian/copyright | 29 ++++++++++++++++++++++++++ debian/rules | 9 ++++++++ debian/source/format | 1 + debian/upstream/metadata | 12 +++++++++++ debian/watch | 3 +++ 8 files changed, 114 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..335d628 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +roary (3.5.7+dfsg-1) UNRELEASED; urgency=low + + * Initial release (Closes: #<bug>) + + -- Sascha Steinbiss <[email protected]> Thu, 17 Dec 2015 15:36:09 +0000 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..b0cff2a --- /dev/null +++ b/debian/control @@ -0,0 +1,54 @@ +Source: roary +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Sascha Steinbiss <[email protected]> +Build-Depends: debhelper (>= 9), + dh-dist-zilla, + libdist-zilla-plugin-podweaver-perl +Build-Depends-Indep: perl +Standards-Version: 3.9.6 +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/ +Homepage: http://sanger-pathogens.github.io/Roary/ + +Package: roary +Architecture: all +Depends: ${perl:Depends}, + ${misc:Depends}, + perl-modules, + bioperl, + libarray-utils-perl, + libenv-path-perl, + libexception-class-perl, + libfile-find-rule-perl, + libfile-slurper-perl, + libfile-which-perl, + libfindbin-libs-perl, + libgraph-perl, + libgraph-readwrite-perl, + liblog-log4perl-perl, + libmoose-perl, + libperlio-utf8-strict-perl, + libtest-most-perl, + libtest-file-perl, + libtest-output-perl, + libtext-csv-perl, + bedtools, + cd-hit, + ncbi-blast+, + mcl, + parallel, + prank, + mafft, + fasttree +Description: high speed stand alone pan genome pipeline + Roary is a high speed stand alone pan genome pipeline, which takes annotated + assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates + the pan genome. Using a standard desktop PC, it can analyse datasets with + thousands of samples, something which is computationally infeasible with + existing methods, without compromising the quality of the results. 128 samples + can be analysed in under 1 hour using 1 GB of RAM and a single processor. + To perform this analysis using existing methods would take weeks and hundreds + of GB of RAM. Roary is not intended for meta-genomics or for comparing + extremely diverse sets of genomes. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..22cc0de --- /dev/null +++ b/debian/copyright @@ -0,0 +1,29 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: Roary +Source: https://github.com/sanger-pathogens/Roary +Files-Excluded: binaries contrib + +Files: * +Copyright: © 2014-2015 Genome Research Limited +License: GPL-3+ + +Files: debian/* +Copyright: © 2015 Sascha Steinbiss <[email protected]> +License: GPL-3+ + +License: GPL-3+ + This package 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 package 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. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/> + . + On Debian systems, the complete text of the GNU General + Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..90bb740 --- /dev/null +++ b/debian/rules @@ -0,0 +1,9 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +%: + dh $@ --with dist-zilla + +override_dh_auto_test: + # pass diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/upstream/metadata b/debian/upstream/metadata new file mode 100644 index 0000000..f39ec1b --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,12 @@ +Reference: + Author: Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill + Title: Roary: Rapid large-scale prokaryote pan genome analysis + Journal: Bioinformatics + Year: 2015 + Volume: 31 + Number: 22 + Pages: 3691-3693 + DOI: 10.1093/bioinformatics/btv421 + PMID: 26198102 + URL: http://bioinformatics.oxfordjournals.org/content/31/22/3691 + eprint: http://bioinformatics.oxfordjournals.org/content/31/22/3691.full.pdf+html diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..b6e401b --- /dev/null +++ b/debian/watch @@ -0,0 +1,3 @@ +version=3 +opts=repacksuffix=+dfsg,dversionmangle=s/\+(debian|dfsg|ds|deb)(\.\d+)?$// \ +https://github.com/sanger-pathogens/roary/tags .*/v?(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz)) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/roary.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
