[med-svn] [phyml] 02/05: Introduce phyml-beagle package

[Andreas Tille]

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tille pushed a commit to branch master
in repository phyml.

commit 593167e8075136e2677ecb67ae1c20ea2771b496
Author: Andreas Tille <tille at debian.org>
Date:   Sat Jun 24 11:10:05 2017 +0200

    Introduce phyml-beagle package
---
 debian/control                       | 30 +++++++++++++++++++++++++++++-
 debian/{links => phyml-beagle.links} |  0
 debian/rules                         | 18 ++++++++++++------
 3 files changed, 41 insertions(+), 7 deletions(-)

diff --git a/debian/control b/debian/control
index 80f3340..afac0c8 100644
--- a/debian/control
+++ b/debian/control
@@ -9,7 +9,7 @@ Build-Depends: debhelper (>= 10),
                autotools-dev,
                dh-autoreconf,
                pkg-config,
-               libhmsbeagle-dev,
+               libhmsbeagle-dev [any-amd64 any-i386 arm64 armhf],
                libopenmpi-dev,
                chrpath
 Standards-Version: 3.9.8
@@ -44,3 +44,31 @@ Description: Phylogenetic estimation using Maximum Likelihood
  character long.
  .
  This package also includes PhyTime.
+
+Package: phyml-beagle
+Architecture: any-amd64 any-i386 arm64 armhf
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         openmpi-bin
+Description: Phylogenetic estimation using Maximum Likelihood
+ PhyML is a software that estimates maximum likelihood phylogenies from
+ alignments of nucleotide or amino acid sequences. It provides a wide
+ range of options that were designed to facilitate standard phylogenetic
+ analyses. The main strengths of PhyML lies in the large number of
+ substitution models coupled to various options to search the space of
+ phylogenetic tree topologies, going from very fast and efficient methods
+ to slower but generally more accurate approaches. It also implements
+ two methods to evaluate branch supports in a sound statistical framework
+ (the non-parametric bootstrap and the approximate likelihood ratio test).
+ .
+ PhyML was designed to process moderate to large data sets. In theory,
+ alignments with up to 4,000 sequences 2,000,000 character-long can
+ be analyzed. In  practice however, the amount of memory required to process
+ a data set is proportional of the product of the number of sequences by their
+ length. Hence, a large number of sequences can only be processed provided
+ that they are short. Also, PhyML can handle long sequences provided that
+ they are not numerous. With most standard personal computers, the “comfort
+ zone” for PhyML generally lies around 3 to 500 sequences less than 2,000
+ character long.
+ .
+ This package contains the hmsbeagle optimisation.
diff --git a/debian/links b/debian/phyml-beagle.links
similarity index 100%
rename from debian/links
rename to debian/phyml-beagle.links
diff --git a/debian/rules b/debian/rules
index e7bd3be..a5d1ebd 100755
--- a/debian/rules
+++ b/debian/rules
@@ -3,7 +3,11 @@
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all,-pie
 
-DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+BUILDARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH)
+
+include /usr/share/dpkg/default.mk
+
+PKGBEAGLE=$(DEB_SOURCE)-beagle
 
 %:
 	dh $@ --with autoreconf
@@ -22,12 +26,14 @@ override_dh_auto_build:
 	# move phyml binary to temporary dir inside debian/
 	mkdir -p $(CURDIR)/debian/bin
 	mv src/phyml $(CURDIR)/debian/bin/phyml
+ifeq ($(BUILDARCH),$(filter $(BUILDARCH), amd64 i386 arm64 armhf))
 	$(MAKE) distclean
 	dh_auto_configure -- --enable-beagle
 	dh_auto_build -- LDFLAGS="$(LDFLAGS)"
 	# move phyml binary to temporary dir inside debian/
-	mkdir -p $(CURDIR)/debian/bin
-	mv src/phyml-beagle $(CURDIR)/debian/bin/phyml-beagle
+	mkdir -p $(CURDIR)/debian/$(PKGBEAGLE)/usr/lib/phyml/bin
+	mv src/phyml-beagle $(CURDIR)/debian/$(PKGBEAGLE)/usr/lib/phyml/bin
+endif
 	$(MAKE) distclean
 	dh_auto_configure -- --enable-mpi
 	dh_auto_build -- LDFLAGS="$(LDFLAGS)"
@@ -42,9 +48,9 @@ override_dh_auto_build:
 override_dh_auto_install:
 	dh_auto_install
 	# install phyml binary we have kept safe above
-	mkdir -p $(CURDIR)/debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)/bin
-	mv $(CURDIR)/debian/bin/* $(CURDIR)/debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)/bin
-	chrpath --delete debian/$(DEBPKGNAME)/usr/lib/$(DEBPKGNAME)/bin/phyml*
+	mkdir -p $(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin
+	mv $(CURDIR)/debian/bin/* $(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin
+	chrpath --delete debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin/phyml*
 
 override_dh_auto_clean:
 	# save pdf from cleaning

-- 
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