[med-svn] [proteinortho] 02/02: Add initial packaging
Andreas Tille
tille at debian.org
Thu Nov 12 11:54:55 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository proteinortho.
commit e55129ab5bd1c4b2a5d58d7356833788aea7a9d2
Author: Andreas Tille <tille at debian.org>
Date: Thu Nov 12 12:54:26 2015 +0100
Add initial packaging
---
debian/README.test | 10 ++++++++++
debian/bin/proteinortho5 | 2 ++
debian/changelog | 5 +++++
debian/clean | 6 ++++++
debian/compat | 1 +
debian/control | 26 ++++++++++++++++++++++++++
debian/copyright | 25 +++++++++++++++++++++++++
debian/dirs | 1 +
debian/docs | 2 ++
debian/examples | 3 +++
debian/install | 1 +
debian/rules | 22 ++++++++++++++++++++++
debian/source/format | 1 +
debian/tests/control | 3 +++
debian/tests/run-unit-test | 17 +++++++++++++++++
debian/upstream/metadata | 11 +++++++++++
debian/watch | 4 ++++
17 files changed, 140 insertions(+)
diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..3d2b347
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,10 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+To run the unit tests provided by the package you can do
+
+ sh run-unit-test
+
+in this directory.
+
+
diff --git a/debian/bin/proteinortho5 b/debian/bin/proteinortho5
new file mode 100644
index 0000000..06c6528
--- /dev/null
+++ b/debian/bin/proteinortho5
@@ -0,0 +1,2 @@
+#!/bin/sh
+/usr/lib/proteinortho/proteinortho5.pl $@
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..feb00d3
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+proteinortho (5.11+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #???)
+
+ -- Andreas Tille <tille at debian.org> Thu, 12 Nov 2015 11:36:14 +0100
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..bbda500
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1,6 @@
+test/*.phr
+test/*.pin
+test/*.psq
+proteinortho5_clean_edges
+proteinortho5_clustering
+test.*
\ No newline at end of file
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..f10d267
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,26 @@
+Source: proteinortho
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ ncbi-blast+
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/proteinortho.git
+Vcs-Git: git://anonscm.debian.org/debian-med/proteinortho.git
+Homepage: https://www.bioinf.uni-leipzig.de/Software/proteinortho/
+
+Package: proteinortho
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ ncbi-blast+,
+ python
+Description: Detection of (Co-)orthologs in large-scale protein analysis
+ Proteinortho is a stand-alone tool that is geared towards large datasets
+ and makes use of distributed computing techniques when run on multi-core
+ hardware. It implements an extended version of the reciprocal best
+ alignment heuristic. Proteinortho was applied to compute orthologous
+ proteins in the complete set of all 717 eubacterial genomes available at
+ NCBI at the beginning of 2009. Authors succeeded identifying thirty
+ proteins present in 99% of all bacterial proteomes.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..238779d
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,25 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Proteinortho
+Upstream-Contact: Marcus Lechner <lechner at staff.uni-marburg.de>
+Source: https://www.bioinf.uni-leipzig.de/Software/proteinortho/
+Files-Excluded: proteinortho5_clean_edges
+ proteinortho5_clustering
+
+Files: *
+Copyright: 2009-2014 Marcus Lechner <lechner at staff.uni-marburg.de>
+License: GPL-2+
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: GPL-2+
+
+License: GPL-2+
+ Proteinortho 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 2, or (at your
+ option) any later version.
+ .
+ Proteinortho 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.
diff --git a/debian/dirs b/debian/dirs
new file mode 100644
index 0000000..d65d9e1
--- /dev/null
+++ b/debian/dirs
@@ -0,0 +1 @@
+usr/lib/proteinortho
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..9a4f4f8
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,2 @@
+debian/README.test
+debian/tests/run-unit-test
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..4fb5d21
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1,3 @@
+test/*.faa
+test/*.gff
+chk_test.pl
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..8e71dae
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+debian/bin usr
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..7641d4e
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,22 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# 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.
+
+%:
+ dh $@
+
+override_dh_auto_install:
+ dh_auto_install --buildsystem=makefile -- install INSTALLDIR=$(CURDIR)/debian/$(DEBPKGNAME)/usr/lib/proteinortho
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..d2aa55a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..7a851b8
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,17 @@
+#!/bin/sh -e
+
+pkg=proteinortho
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+mkdir test
+cp -a /usr/share/doc/${pkg}/examples/* test
+find . -type f -name "*.gz" -exec gunzip \{\} \;
+mv test/chk_test.pl .
+proteinortho5 -project=test -synteny -singles test/*.faa
+./chk_test.pl test.proteinortho
+./chk_test.pl test.poff
+echo "Test okay"
+
+rm -fr $ADTTMP/*
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..b33b838
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Reference:
+ Author: Marcus Lechner and Sven Findeiß and Lydia Steiner and Manja Marz and Peter F Stadler and Sonja J Prohaska
+ Title: "Proteinortho: Detection of (Co-)orthologs in large-scale analysis"
+ Journal: BMC Bioinformatics
+ Year: 2011
+ Volume: 12
+ Pages: 124
+ DOI: 10.1186/1471-2105-12-124
+ PMID: 21526987
+ URL: http://www.biomedcentral.com/1471-2105/12/124
+ eprint: http://www.biomedcentral.com/content/pdf/1471-2105-12-124.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..21751b3
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+ http://www.bioinf.uni-leipzig.de/Software/proteinortho/ proteinortho_v([\d.]+)\.tar\.gz
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/proteinortho.git
More information about the debian-med-commit
mailing list