[med-svn] [examl] 02/02: Add initial packaging
Andreas Tille
tille at debian.org
Wed Feb 15 16:08:47 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository examl.
commit f2e0353db12fa7be29d5bdc743fdb7a94ad1bc5d
Author: Andreas Tille <tille at debian.org>
Date: Wed Feb 15 17:08:10 2017 +0100
Add initial packaging
---
debian/bin/examl | 22 ++++++++++++++++++++++
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 26 ++++++++++++++++++++++++++
debian/copyright | 11 +++++++++++
debian/install | 4 ++++
debian/links | 4 ++++
debian/rules | 34 ++++++++++++++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 3 +++
11 files changed, 123 insertions(+)
diff --git a/debian/bin/examl b/debian/bin/examl
new file mode 100755
index 0000000..ce6b820
--- /dev/null
+++ b/debian/bin/examl
@@ -0,0 +1,22 @@
+#!/bin/sh
+
+EXAMLDIR=/usr/lib/examl/bin
+NPROC=`nproc`
+
+if grep -q avx /proc/cpuinfo; then
+ if [ $NPROC -gt 1 ] ; then
+ echo "Use examl with OMP and AVX support"
+ ${EXAMLDIR}/examl-OMP-AVX "$@"
+ else
+ echo "Use examl with AVX support without OMP"
+ ${EXAMLDIR}/examl-AVX "$@"
+ fi
+else
+ if [ $NPROC -gt 1 ] ; then
+ echo "Use examl with AVX support with overriden number of threads"
+ ${EXAMLDIR}/examl-OMP "$@"
+ else
+ echo "Use plain examl without AVX and OMP"
+ ${EXAMLDIR}/examl "$@"
+ fi
+fi
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..c99bd31
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+examl (3.0.18-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 14 Feb 2017 17:37:55 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..b519b51
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,26 @@
+Source: examl
+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 (>= 10),
+ libopenmpi-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/examl.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/examl.git
+Homepage: https://github.com/stamatak/ExaML
+
+Package: examl
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
+ Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
+ using MPI.
+ .
+ This code implements the popular RAxML search algorithm for maximum
+ likelihood based inference of phylogenetic trees.
+ .
+ It uses a radically new MPI parallelization approach that yields
+ improved parallel efficiency, in particular on partitioned multi-gene or
+ whole-genome datasets.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..3416315
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,11 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: <pkg>
+Source: <path_to_download>
+
+Files: *
+Copyright: © 20xx-20yy <upstream>
+License: <license>
+
+Files: debian/*
+Copyright: © 2016 maintainername <maintainer at e.mail>
+License: <license>
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..a3083b5
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,4 @@
+examl/examl usr/lib/examl/bin
+examl/examl-* usr/lib/examl/bin
+debian/bin usr
+
diff --git a/debian/links b/debian/links
new file mode 100644
index 0000000..d9b57b6
--- /dev/null
+++ b/debian/links
@@ -0,0 +1,4 @@
+usr/lib/examl/bin/examl-AVX usr/bin/examl-AVX
+usr/lib/examl/bin/examl-OMP usr/bin/examl-OMP
+usr/lib/examl/bin/examl-OMP-AVX usr/bin/examl-OMP-AVX
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..de04100
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,34 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+# 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.
+
+# for hardening you might like to uncomment this:
+# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+MFILES:=$(shell cd examl && ls *.gcc)
+SRCDIR:=examl
+
+%:
+ dh $@ --sourcedirectory=$(SRCDIR)
+
+override_dh_auto_clean:
+ dh_auto_clean
+ for mfile in $(MFILES); do $(MAKE) --directory=$(SRCDIR) -f $${mfile} clean ; done
+
+override_dh_auto_build:
+ dh_auto_build
+ for mfile in $(MFILES); do $(MAKE) --directory=$(SRCDIR) -f $${mfile} ; done
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..b3adba0
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Alexey M. Kozlov and Andre J. Aberer and Alexandros Stamatakis
+ Title: "ExaML version 3: a tool for phylogenomic analyses on supercomputers"
+ Journal: Bioinformatics
+ Year: 2015
+ Volume: 31
+ Number: 15
+ Pages: 2577-2579
+ DOI: 10.1093/bioinformatics/btv184
+ PMID: 25819675
+ URL: https://academic.oup.com/bioinformatics/article/31/15/2577/188794/ExaML-version-3-a-tool-for-phylogenomic-analyses
+ eprint: https://academic.oup.com/bioinformatics/article-pdf/31/15/2577/5030920/btv184.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..91fb388
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+
+https://github.com/stamatak/ExaML/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/examl.git
More information about the debian-med-commit
mailing list