This is an automated email from the git hooks/post-receive script. afif pushed a commit to branch master in repository scoary.
commit f44142cbd8c5d2ac4065472944c6235b1ba98a88 Author: Afif Elghraoui <[email protected]> Date: Sun Jan 15 17:05:53 2017 -0800 Initial packaging --- debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 30 ++++++++++++++++++++++++++++++ debian/copyright | 27 +++++++++++++++++++++++++++ debian/desktop/scoary.desktop | 12 ++++++++++++ debian/docs | 1 + debian/install | 1 + debian/manpages | 1 + debian/rules | 7 +++++++ debian/scoary.1 | 20 ++++++++++++++++++++ debian/source/format | 1 + debian/tests/control | 1 + debian/upstream/metadata | 9 +++++++++ debian/watch | 5 +++++ 14 files changed, 121 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..bc23051 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +scoary (1.6.9-1) UNRELEASED; urgency=medium + + * Initial release (Closes: #nnnn) + + -- Afif Elghraoui <[email protected]> Sun, 15 Jan 2017 15:16:03 -0800 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..3822f63 --- /dev/null +++ b/debian/control @@ -0,0 +1,30 @@ +Source: scoary +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Afif Elghraoui <[email protected]> +Build-Depends: + debhelper (>=9), + dh-python, + python-all, + python-setuptools, + python-scipy (>= 0.16), +# Test-Depends: + python-nose, +Standards-Version: 3.9.8 +Homepage: https://github.com/AdmiralenOla/Scoary +Vcs-Git: https://anonscm.debian.org/debian-med/scoary.git +Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/scoary.git + +Package: scoary +Architecture: all +Depends: + ${misc:Depends}, + ${python:Depends}, + python-pkg-resources, +Suggests: roary +Description: pangenome-wide association studies + Scoary is designed to take the gene_presence_absence.csv file from + Roary as well as a traits file created by the user and calculate the + associations between all genes in the accessory genome and the traits. It + reports a list of genes sorted by strength of association per trait. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..cb3ae1d --- /dev/null +++ b/debian/copyright @@ -0,0 +1,27 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: Scoary +Source: https://github.com/AdmiralenOla/Scoary + +Files: * +Copyright: 2016-2017 Ola Brynildsrud <[email protected]> +License: GPL-3.0 + +Files: debian/* +Copyright: 2017 Afif Elghraoui <[email protected]> +License: GPL-3.0 + +License: GPL-3.0 + 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. + . + 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 <https://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/desktop/scoary.desktop b/debian/desktop/scoary.desktop new file mode 100644 index 0000000..38d326a --- /dev/null +++ b/debian/desktop/scoary.desktop @@ -0,0 +1,12 @@ +[Desktop Entry] +Comment=Pangenome-wide association studies +Exec=scoary_GUI +GenericName[en_US]=Scoary +GenericName=Scoary +Name[en_US]=Scoary +Name=Scoary +Categories=Science;Biology;DataVisualization; +StartupNotify=false +Terminal=false +Type=Application +Keywords=genomics diff --git a/debian/docs b/debian/docs new file mode 100644 index 0000000..b43bf86 --- /dev/null +++ b/debian/docs @@ -0,0 +1 @@ +README.md diff --git a/debian/install b/debian/install new file mode 100644 index 0000000..6339bec --- /dev/null +++ b/debian/install @@ -0,0 +1 @@ +debian/desktop/* usr/share/applications/ diff --git a/debian/manpages b/debian/manpages new file mode 100644 index 0000000..f227160 --- /dev/null +++ b/debian/manpages @@ -0,0 +1 @@ +debian/scoary.1 diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..872142f --- /dev/null +++ b/debian/rules @@ -0,0 +1,7 @@ +#!/usr/bin/make -f + +#export DH_VERBOSE = 1 +export LC_ALL = C.UTF-8 + +%: + dh $@ --with python2 --buildsystem=pybuild diff --git a/debian/scoary.1 b/debian/scoary.1 new file mode 100644 index 0000000..f7459b3 --- /dev/null +++ b/debian/scoary.1 @@ -0,0 +1,20 @@ +.TH SCOARY 1 "January 2017" +.SH NAME +scoary \- pangenome\-wide association studies +.SH SYNOPSIS +.B scoary +.RI [ options ] " files" ... +.SH DESCRIPTION +\fBscoary\fP is designed to take the gene_presence_absence.csv file from +.BR roary (1) +as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome and the traits. +It reports a list of genes sorted by strength of association per trait. +.SH OPTIONS +For a complete usage description, see the help menu. +.TP +.B \-h, \-\-help +Show summary of options. +.SH SEE ALSO +.BR roary (1) +.br +/usr/share/doc/scoary/README.md.gz 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/tests/control b/debian/tests/control new file mode 100644 index 0000000..220a861 --- /dev/null +++ b/debian/tests/control @@ -0,0 +1 @@ +Test-Command: cd $ADTTMP && scoary --test diff --git a/debian/upstream/metadata b/debian/upstream/metadata new file mode 100644 index 0000000..23eceea --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,9 @@ +Reference: + Author: Ola Brynildsrud and Jon Bohlin and Lonneke Scheffer and Vegard Eldholm + Title: Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary + Journal: Genome Biology + Year: 2016 + Volume: 17 + Number: 238 + DOI: 10.1186/s13059-016-1108-8 + URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1108-8 diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..da7ee90 --- /dev/null +++ b/debian/watch @@ -0,0 +1,5 @@ +version=4 + +opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%scoary-$1.tar.gz%" \ + https://github.com/AdmiralenOla/Scoary/tags \ + (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/scoary.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
