[med-svn] [lambda-align] 02/15: debian/ skeleton
Sascha Steinbiss
satta at debian.org
Fri Aug 19 16:10:04 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository lambda-align.
commit 95506bf58ac88f662b4cf826a53cc35a85cbaf02
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Sun Mar 13 14:09:21 2016 +0000
debian/ skeleton
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 22 ++++++++++++++++++++++
debian/copyright | 31 +++++++++++++++++++++++++++++++
debian/doc-base | 20 ++++++++++++++++++++
debian/get-orig-source | 48 ++++++++++++++++++++++++++++++++++++++++++++++++
debian/itp.txt | 21 +++++++++++++++++++++
debian/rules | 25 +++++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 3 +++
11 files changed, 189 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..a2ded5d
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+lambda-align (0.9.3+ds-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Sun, 13 Mar 2016 13:08:34 +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..c6f7dc1
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,22 @@
+Source: lambda-align
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
+Build-Depends: debhelper (>= 9),
+ seqan-dev,
+ cmake
+Standards-Version: 3.9.7
+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: https://seqan.github.io/lambda
+
+Package: lambda-align
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Local Aligner for Massive Biological DatA
+ Lambda is a local biosequence aligner optimized for many query sequences
+ and searches in protein space. It is compatible to the de facto standard tool
+ BLAST, but often outperforms the best currently available alternatives at
+ reproducing BLAST’s results and is the fastest compared with the current
+ state of the art at comparable levels of sensitivity.
\ No newline at end of file
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..f128970
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,31 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: lambda
+Source: https://github.com/seqan/lambda
+Files-Excluded: include/seqan/apps
+ include/seqan/demos
+ include/seqan/dox
+ include/seqan/include
+ include/seqan/manual
+ include/seqan/tests
+ include/seqan/util/bin
+ include/seqan/util/headers
+ include/seqan/util/images
+ include/seqan/util/mingw
+ include/seqan/util/ports
+ include/seqan/util/py_lib
+ include/seqan/util/skel
+ include/seqan/util/travis
+ include/seqan/util/uncrustify
+ include/seqan/util/valgrind
+ include/seqan/.git*
+ include/seqan/CHANGELOG.rst
+ include/seqan/CMakeLists.txt
+ include/seqan/README.rst
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: © 2016 maintainername <maintainer at e.mail>
+License: <license>
diff --git a/debian/doc-base b/debian/doc-base
new file mode 100644
index 0000000..5e7e1d4
--- /dev/null
+++ b/debian/doc-base
@@ -0,0 +1,20 @@
+Document: <pkg>
+Title: <title for this doc>
+Author: <author of this doc>
+Abstract: <if you have no better clue the short and
+ long description from debian/control might fit here as well>
+Section: Science/{Biology,Medicine} # see /usr/share/doc/doc-base/doc-base.txt.gz "2.3.3. The `section' field"
+
+# pick one of the below options
+Format: Text
+Files: /usr/share/doc/<pkg>/<pkg>.txt.gz
+
+Format: html
+Index: /usr/share/doc/<pkg>/html/index.html
+Files: /usr/share/doc/<pkg>/html/*
+
+Format: pdf
+Files: /usr/share/doc/<pkg>/<pkg>.pdf.gz
+
+Format: postscript
+Files: /usr/share/doc/<pkg>/<pkg>.ps.gz
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..fe60132
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,48 @@
+#!/bin/sh
+# if you need to repack for whatever reason you can
+# use this script via uscan or directly
+#
+# FIXME: currently the code is not conform to Debian Policy
+# http://www.debian.org/doc/debian-policy/ch-source.html
+# "get-orig-source (optional)"
+# This target may be invoked in any directory, ...
+# --> currently it is assumed the script is called in the
+# source directory featuring the debian/ dir
+
+# For an example how to fetch source from sourceforge SVN see
+# git://anonscm.debian.org/debian-med/kmer-tools.git
+
+COMPRESS=xz
+
+set -e
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+
+if ! echo $@ | grep -q upstream-version ; then
+ VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+ uscan --force-download
+else
+ VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${NAME}.*?\1?"`
+ if echo "$VERSION" | grep -q "upstream-version" ; then
+ echo "Unable to parse version number"
+ exit
+ fi
+fi
+
+TARDIR=${NAME}-${VERSION}
+mkdir -p ../tarballs
+cd ../tarballs
+# need to clean up the tarballs dir first because upstream tarball might
+# contain a directory with unpredictable name
+rm -rf *
+tar -xaf ../${TARDIR}.tar.gz
+
+UPSTREAMTARDIR=`find . -mindepth 1 -maxdepth 1 -type d`
+if [ "${UPSTREAMTARDIR}" != "${TARDIR}" ] ; then
+ mv "${UPSTREAMTARDIR}" "${TARDIR}"
+fi
+
+# Remove useless binaries
+# ... do something which needs to be done ...
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}
diff --git a/debian/itp.txt b/debian/itp.txt
new file mode 100644
index 0000000..17950e4
--- /dev/null
+++ b/debian/itp.txt
@@ -0,0 +1,21 @@
+Subject: ITP: lambda-align -- Local Aligner for Massive Biological DatA
+Package: wnpp
+Owner: Sascha Steinbiss <satta at tetrinetsucht.de>
+Severity: wishlist
+X-Debbugs-CC: debian-med at lists.debian.org
+
+* Package name : lambda-align
+ Version : 0.9.3
+ Upstream Author : Hannes Hauswedell <hannes.hauswedell at fu-berlin.de>
+* URL : https://seqan.github.io/lambda
+* License : GPL
+ Programming Lang: C++
+ Description : Local Aligner for Massive Biological DatA
+
+Lambda is a local biosequence aligner optimized for many query sequences
+and searches in protein space. It is compatible to the de facto standard tool
+BLAST, but often outperforms the best currently available alternatives at
+reproducing BLAST’s results and is the fastest compared with the current
+state of the art at comparable levels of sensitivity.
+
+This package will be maintained under the umbrella of the Debian Med Team.
\ No newline at end of file
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..2d9e6ea
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,25 @@
+#!/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 $@
+
+override_dh_auto_build:
+ mkdir build
+ cd build
+ cmake ../lambda-v$(VERSION)
+ make
\ No newline at end of file
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..d8b5812
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author:
+ Title:
+ Journal:
+ Year:
+ Volume:
+ Number:
+ Pages:
+ DOI:
+ PMID:
+ URL:
+ eprint:
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..e3383c6
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+opts=repacksuffix=+ds,dversionmangle=s/\+(debian|dfsg|ds|deb)(\.\d+)?$//,repack,compression=xz \
+https://github.com/seqan/lambda/tags .*/lambda-v?(\d.*)\.tar.gz
--
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