[med-svn] [seqan] 09/14: Revert "Symlink to binaries only if these are part of the binary distribution"
Andreas Tille
tille at debian.org
Tue Jul 26 07:29:22 UTC 2016
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tille pushed a commit to branch master
in repository seqan.
commit cf786e8eb0291810ebe30060df5a1c690cc05d6c
Author: Andreas Tille <tille at debian.org>
Date: Tue Jul 26 09:28:21 2016 +0200
Revert "Symlink to binaries only if these are part of the binary distribution"
This reverts commit f36ba41118b33e69b68c63bb2e508b37162a385b.
---
debian/changelog | 1 -
debian/rules | 31 +++++++------------------------
debian/seqan-apps.links | 21 +++++++++++++++++++++
3 files changed, 28 insertions(+), 25 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 449f39e..2a639c2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -16,7 +16,6 @@ seqan (2.0.1+dfsg-1) UNRELEASED; urgency=medium
else and should be moved to a separate package
* New package seqan-doc
* Moved to Git
- * Symlink to binaries only if these are part of the binary distribution
-- Andreas Tille <tille at debian.org> Mon, 18 Jan 2016 15:00:43 +0100
diff --git a/debian/rules b/debian/rules
index 0c9e5fb..4520c6c 100755
--- a/debian/rules
+++ b/debian/rules
@@ -22,9 +22,6 @@ ifneq (,$(filter $(DEB_BUILD_ARCH),mips mipsel))
export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS | sed 's/-O[1-9]//') -O0 -mxgot
endif
-pkgapps=seqan-apps
-pkgdev=seqan-dev
-
%:
dh $@ --parallel
@@ -37,14 +34,14 @@ override_dh_install:
# /usr/bin/join is part of coreutils package: Avoid name conflict by renaming it to seqan-join
# This solution is withdrawn in favour of just providing a set of binaries according to upstream
# in /usr/bin (via symlink) while others go to /usr/lib/seqan/bin (see README.Debian)
- # mv $(CURDIR)/debian/$(pkgapps)/usr/bin/join $(CURDIR)/debian/$(pkgapps)/usr/bin/seqan-join
+ # mv $(CURDIR)/debian/seqan-apps/usr/bin/join $(CURDIR)/debian/seqan-apps/usr/bin/seqan-join
#
# Formerly binaries were installed into usr/lib/seqan/bin/
# and only some of them were made available in /usr/bin via dh_link
# Since there is no obvious reason for this neither is there any
# documentation that explains the motivation this is commented here.
#for APP in `find $(CURDIR)/obj*/apps -mindepth 1 -maxdepth 1 -executable -type f` ; do \
- # cp -a $$APP $(CURDIR)/debian/$(pkgapps)/usr/lib/seqan/bin/ ; done
+ # cp -a $$APP $(CURDIR)/debian/seqan-apps/usr/lib/seqan/bin/ ; done
# ------------------------------------------------------------------
# Formerly readmes were named README.app. It seems more consistent
# to keep upstream documentation layout which in addition contains
@@ -52,14 +49,14 @@ override_dh_install:
#for APP in `find apps -name README` ; do \
# app=`echo $$APP | sed 's?.*apps/\(.\+\)/README?\1?'` ; \
# echo $$app ; \
- # cp -a $$APP $(CURDIR)/debian/$(pkgapps)/usr/share/doc/$(pkgapps)/README.$$app ; \
+ # cp -a $$APP $(CURDIR)/debian/seqan-apps/usr/share/doc/seqan-apps/README.$$app ; \
#done
# ------------------------------------------------------------------
# Delete additional LICENSE files
- find $(CURDIR)/debian/$(pkgapps) -type f -name LICENSE -delete
- if [ -d $(CURDIR)/debian/$(pkgdev) ] ; then \
- find $(CURDIR)/debian/$(pkgdev) -type f -name LICENSE -delete ; \
- find $(CURDIR)/debian/$(pkgdev) -type f -name "*.pyc" -delete ; \
+ find $(CURDIR)/debian/seqan-apps -type f -name LICENSE -delete
+ if [ -d $(CURDIR)/debian/seqan-dev ] ; then \
+ find $(CURDIR)/debian/seqan-dev -type f -name LICENSE -delete ; \
+ find $(CURDIR)/debian/seqan-dev -type f -name "*.pyc" -delete ; \
fi
override_dh_auto_clean:
@@ -74,24 +71,10 @@ override_dh_auto_clean:
override_dh_link:
dh_link
- for bin in `ls $(CURDIR)/$(pkgapps)/usr/lib/seqan/bin` ; do \
- if [ -x $(CURDIR)/$(pkgapps)/usr/lib/seqan/bin/$${bin} ] ; then \
- ln -s ../lib/seqan/bin/$${bin} $(CURDIR)/$(pkgapps)/usr/bin/$${bin} ; \
- fi ; \
- if echo $${bin} | grep -q '\.sh$' ; then \
- ln -s ../lib/seqan/bin/$${bin} $(CURDIR)/$(pkgapps)/usr/bin/`basename $${bin} .sh` ; \
- fi ; \
- done
# we generate only those manpages where binaries are linked to /usr/bin
# since dh_link is executed after dh_installmanpages this is done here
$(CURDIR)/debian/generate_manpages
-override_dh_fixperms:
- dh_fixperms
- for bin in `ls $(CURDIR)/$(pkgapps)/usr/lib/seqan/bin/*.sh` ; do \
- chmod +x $(CURDIR)/$(pkgapps)/usr/lib/seqan/bin/$${bin} ; \
- done
-
override_dh_auto_test:
# Run test suite only on powerfull architectures (amd64) at build time
ifneq (,$(filter $(DEB_HOST_ARCH),amd64 kfreebsd-amd64))
diff --git a/debian/seqan-apps.links b/debian/seqan-apps.links
new file mode 100644
index 0000000..bb7fb5b
--- /dev/null
+++ b/debian/seqan-apps.links
@@ -0,0 +1,21 @@
+usr/lib/seqan/bin/alf usr/bin/alf
+usr/lib/seqan/bin/gustaf usr/bin/gustaf
+usr/lib/seqan/bin/insegt usr/bin/insegt
+usr/lib/seqan/bin/masai_indexer usr/bin/masai_indexer
+usr/lib/seqan/bin/masai_mapper usr/bin/masai_mapper
+usr/lib/seqan/bin/masai_output_pe usr/bin/masai_output_pe
+usr/lib/seqan/bin/masai_output_se usr/bin/masai_output_se
+usr/lib/seqan/bin/mason usr/bin/seqan_mason
+usr/lib/seqan/bin/micro_razers usr/bin/micro_razers
+usr/lib/seqan/bin/pair_align usr/bin/pair_align
+usr/lib/seqan/bin/rabema_build_gold_standard usr/bin/rabema_build_gold_standard
+usr/lib/seqan/bin/rabema_evaluate usr/bin/rabema_evaluate
+usr/lib/seqan/bin/rabema_prepare_sam usr/bin/rabema_prepare_sam
+usr/lib/seqan/bin/razers usr/bin/razers
+usr/lib/seqan/bin/razers3 usr/bin/razers3
+usr/lib/seqan/bin/sak usr/bin/sak
+usr/lib/seqan/bin/seqan_tcoffee usr/bin/seqan_tcoffee
+usr/lib/seqan/bin/snp_store usr/bin/snp_store
+usr/lib/seqan/bin/splazers usr/bin/splazers
+usr/lib/seqan/bin/stellar usr/bin/stellar
+usr/lib/seqan/bin/tree_recon usr/bin/tree_recon
--
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