[med-svn] [spades] 08/08: use wrapper

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository spades.

commit a43a86b792d04d1af074ed6df5ab8e949858687d
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Thu Feb 11 11:32:57 2016 +0000

    use wrapper
---
 debian/links | 11 ++++++-----
 debian/rules | 43 ++++++++-----------------------------------
 2 files changed, 14 insertions(+), 40 deletions(-)

diff --git a/debian/links b/debian/links
index 978cfb3..c676348 100644
--- a/debian/links
+++ b/debian/links
@@ -1,5 +1,6 @@
-#usr/bin/spades					usr/bin/dipspades
-#usr/lib/spades/share/spades/test_dataset	usr/share/doc/spades/examples
-#usr/bin/bwa					usr/bin/bwa-spades
-#etc/spades					usr/share/spades/configs
-#usr/share					usr/lib/spades/share
+usr/bin/spades  usr/bin/spades.py
+usr/bin/spades  usr/bin/spades
+usr/bin/spades  usr/bin/dipspades.py
+usr/bin/spades  usr/bin/dipspades
+usr/bin/spades  usr/bin/truspades.py
+usr/bin/spades  usr/bin/truspades
\ No newline at end of file
diff --git a/debian/rules b/debian/rules
index 7e40235..bf44887 100755
--- a/debian/rules
+++ b/debian/rules
@@ -8,6 +8,7 @@ CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) $(CPPFLAGS)
 LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
 DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
 TMPDIR     := $(CURDIR)/install_spades
+LIBDIR     := debian/$(DEBPKGNAME)/usr/lib/spades
 
 PREFIX:=/usr
 BUILD_DIR:=$(CURDIR)/build_spades
@@ -41,44 +42,16 @@ override_dh_auto_install:
 
 override_dh_install:
 	dh_install
-	# move those binaries away from /usr/bin that do not need to be called explicitly
-	#mkdir -p $(LIBDIR)
-	#mv debian/$(DEBPKGNAME)/usr/bin $(LIBDIR)
-	#mkdir -p $(LIBDIR)/share
-	#mv $(SHAREDIR) $(LIBDIR)/share
-	#for pyfile in `ls $(LIBDIR)/bin/*.py` ; do \
-	#    mv $$pyfile $(SHAREDIR) ; \
-	#    ln -s ../../../share/$(DEBPKGNAME)/`basename $$pyfile` $(LIBDIR)/bin/`basename $$pyfile` ; \
-	#done
-	#touch $(SHAREDIR)/spades_pipeline/__init__.py
-	# install wrapper
-	#cp -a debian/bin debian/$(DEBPKGNAME)/usr/
-	# delete duplicate of license
-	find debian -type f -name GPLv2.txt -delete
-	find debian -type f -name LICENSE -delete
-	#
-	# for some strange reason the test suite fails if bwa is not build
-	# we just do not install it but rather remove the executable from
-	# installation dir and replace it by a link to the Debian packaged bwa
-	find debian -type f -name bwa-spades -delete
-	# sort out config files
-	#for cfile in `find debian/$(DEBPKGNAME)/etc -name "*.template"` ; do \
-	#    ifile=`echo $${cfile} | sed 's/\.template$$//'` ; \
-	#    if [ -e $${ifile} ] ; then \
-	#        rm -f $${cfile} ; \
-	#    else \
-	#        mv $${cfile} $${ifile} ; \
-	#    fi ; \
-	#done
-	#find debian/$(DEBPKGNAME)/etc -name "*.i" -delete
-	#find debian/$(DEBPKGNAME)/etc -name "*.propertie" -delete
-	# remove config templates
-	#rm -rf debian/$(DEBPKGNAME)/usr/share/$(DEBPKGNAME)/configs
+	mkdir -p $(LIBDIR)
+	mv debian/$(DEBPKGNAME)/usr/bin $(LIBDIR)
+	mkdir -p debian/$(DEBPKGNAME)/usr/bin
+	install debian/bin/spades debian/$(DEBPKGNAME)/usr/bin/
+	chmod +x debian/$(DEBPKGNAME)/usr/bin/spades
+	rm -f debian/$(DEBPKGNAME)/usr/share/spades/GPLv2.txt
+	rm -f debian/$(DEBPKGNAME)/usr/share/spades/LICENSE
 
 override_dh_installdocs:
 	dh_installdocs
-	# move documentation
-	#find debian/$(DEBPKGNAME)/usr -type f -name "*.html" -exec mv \{\} debian/$(DEBPKGNAME)/usr/share/doc/$(DEBPKGNAME) \;
 
 override_dh_installchangelogs:
 	lynx -dump changelog.html > changelog

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