[med-svn] r14448 - in trunk/packages/hmmer/trunk/debian: . patches
Timothy Booth
tbooth-guest at alioth.debian.org
Thu Aug 15 15:45:50 UTC 2013
Author: tbooth-guest
Date: 2013-08-15 15:45:50 +0000 (Thu, 15 Aug 2013)
New Revision: 14448
Added:
trunk/packages/hmmer/trunk/debian/patches/fix_clean_target
Removed:
trunk/packages/hmmer/trunk/debian/hmmer.manpages
Modified:
trunk/packages/hmmer/trunk/debian/changelog
trunk/packages/hmmer/trunk/debian/control
trunk/packages/hmmer/trunk/debian/hmmer.install
trunk/packages/hmmer/trunk/debian/patches/debian-changes-3.0-1
trunk/packages/hmmer/trunk/debian/patches/debian-changes-3.0-2.1
trunk/packages/hmmer/trunk/debian/patches/series
trunk/packages/hmmer/trunk/debian/rules
trunk/packages/hmmer/trunk/debian/watch
Log:
I've packaged the latest hmmer for Bio-Linux/Ubuntu LTS.
Note that despite having a 'b' in the version it is on the website as a stable
release. I've modified the watchfile to spot it.
I switched from CDBS to DH as I can't get on with CDBS and modifications
were required to make the build happy. Apologies to the
maintainers if you don't like this but if you don't like it you can always revert
(to r14447).
Modified: trunk/packages/hmmer/trunk/debian/changelog
===================================================================
--- trunk/packages/hmmer/trunk/debian/changelog 2013-08-15 12:44:25 UTC (rev 14447)
+++ trunk/packages/hmmer/trunk/debian/changelog 2013-08-15 15:45:50 UTC (rev 14448)
@@ -1,3 +1,21 @@
+hmmer (3.1b1-0biolinux1) precise; urgency=low
+
+ * New upstream
+ * Switch to DH in rules as CDBS does my nut in
+ * Simplify hmmer.install and kill hmmer.manpages
+ * Added binaries:
+ alimask
+ hmmc2
+ hmmlogo
+ hmmpgmd
+ nhmmer
+ nhmmscan
+ * Modify watchfile to see new version
+ * Avoid compressing all the tutorial data
+ * make distclean was failing :- fixed with patch
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Thu, 15 Aug 2013 16:34:31 +0100
+
hmmer (3.0-4) unstable; urgency=low
[ Charles Plessy ]
Modified: trunk/packages/hmmer/trunk/debian/control
===================================================================
--- trunk/packages/hmmer/trunk/debian/control 2013-08-15 12:44:25 UTC (rev 14447)
+++ trunk/packages/hmmer/trunk/debian/control 2013-08-15 15:45:50 UTC (rev 14448)
@@ -7,8 +7,9 @@
Nelson A. de Oliveira <naoliv at debian.org>,
Andreas Tille <tille at debian.org>,
Charles Plessy <plessy at debian.org>,
- Eric Talevich <etal at uga.edu>
-Build-Depends: cdbs, debhelper (>= 8), autotools-dev
+ Eric Talevich <etal at uga.edu>,
+ Tim Booth <tbooth at ceh.ac.uk>
+Build-Depends: debhelper (>= 8), autotools-dev
Standards-Version: 3.9.3
Homepage: http://hmmer.janelia.org/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/hmmer/trunk/
@@ -32,7 +33,7 @@
Section: doc
Architecture: all
Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: hmmer (>= ${source:Version}), xpdf-reader | pdf-viewer
+Recommends: hmmer (>= ${source:Version}), pdf-viewer | xpdf-reader
Description: profile hidden Markov models for protein sequence analysis (docs)
HMMER is an implementation of profile hidden Markov model methods for
sensitive searches of biological sequence databases using multiple sequence
Modified: trunk/packages/hmmer/trunk/debian/hmmer.install
===================================================================
--- trunk/packages/hmmer/trunk/debian/hmmer.install 2013-08-15 12:44:25 UTC (rev 14447)
+++ trunk/packages/hmmer/trunk/debian/hmmer.install 2013-08-15 15:45:50 UTC (rev 14448)
@@ -1,12 +1,2 @@
-debian/tmp/usr/bin/hmmalign
-debian/tmp/usr/bin/hmmbuild
-debian/tmp/usr/bin/hmmconvert
-debian/tmp/usr/bin/hmmemit
-debian/tmp/usr/bin/hmmfetch
-debian/tmp/usr/bin/hmmpress
-debian/tmp/usr/bin/hmmscan
-debian/tmp/usr/bin/hmmsearch
-debian/tmp/usr/bin/hmmsim
-debian/tmp/usr/bin/hmmstat
-debian/tmp/usr/bin/jackhmmer
-debian/tmp/usr/bin/phmmer
+usr/bin
+usr/share/man
Deleted: trunk/packages/hmmer/trunk/debian/hmmer.manpages
===================================================================
--- trunk/packages/hmmer/trunk/debian/hmmer.manpages 2013-08-15 12:44:25 UTC (rev 14447)
+++ trunk/packages/hmmer/trunk/debian/hmmer.manpages 2013-08-15 15:45:50 UTC (rev 14448)
@@ -1,14 +0,0 @@
-debian/tmp/usr/share/man/man1/hmmbuild.1
-debian/tmp/usr/share/man/man1/hmmpress.1
-debian/tmp/usr/share/man/man1/hmmsearch.1
-debian/tmp/usr/share/man/man1/hmmscan.1
-debian/tmp/usr/share/man/man1/hmmer.1
-debian/tmp/usr/share/man/man1/hmmconvert.1
-debian/tmp/usr/share/man/man1/hmmalign.1
-debian/tmp/usr/share/man/man1/hmmsim.1
-debian/tmp/usr/share/man/man1/phmmer.1
-debian/tmp/usr/share/man/man1/jackhmmer.1
-debian/tmp/usr/share/man/man1/hmmfetch.1
-debian/tmp/usr/share/man/man1/hmmemit.1
-debian/tmp/usr/share/man/man1/hmmstat.1
-
Modified: trunk/packages/hmmer/trunk/debian/patches/debian-changes-3.0-1
===================================================================
--- trunk/packages/hmmer/trunk/debian/patches/debian-changes-3.0-1 2013-08-15 12:44:25 UTC (rev 14447)
+++ trunk/packages/hmmer/trunk/debian/patches/debian-changes-3.0-1 2013-08-15 15:45:50 UTC (rev 14448)
@@ -24,42 +24,14 @@
Reviewed-By: <name and email of someone who approved the patch>
Last-Update: <YYYY-MM-DD>
---- hmmer-3.0.orig/Makefile.in
-+++ hmmer-3.0/Makefile.in
-@@ -39,7 +39,7 @@ datarootdir = @datarootdir@
- bindir = @bindir@
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -47,7 +47,7 @@
+ pdfdir = @pdfdir@
mandir = @mandir@
man1dir = ${mandir}/man1
--manext = .1
-+manext = 1
+-man1ext = .1
++man1ext = 1
# Compiler configuration
#
-@@ -180,10 +180,10 @@ install: libraries programs
- for file in $(PROGS); do\
- cp ${SRCDIR}/$$file ${DESTDIR}${bindir}/;\
- done
--# -mkdir -p ${DESTDIR}/${MANDIR}/man${MANSUFFIX}
--# -for file in hmmer $(PROGS); do\
--# $(INSTMAN) documentation/man/$$file.man ${DESTDIR}$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
--# done
-+ -mkdir -p ${DESTDIR}/${mandir}/man${manext}
-+ -for file in hmmer $(PROGS); do\
-+ $(INSTMAN) documentation/man/$$file.man ${DESTDIR}${mandir}/man${manext}/$$file.${manext};\
-+ done
-
- # uninstall: Reverses the steps of "make install".
- #
-@@ -191,9 +191,9 @@ uninstall:
- for file in $(PROGS); do\
- rm ${DESTDIR}${bindir}/$$file;\
- done
--# for file in hmmer $(PROGS); do\
--# rm $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
--# done
-+ for file in hmmer $(PROGS); do\
-+ rm $(MANDIR)/man$(manext)/$$file.$(manext);\
-+ done
-
-
- # "make clean" removes almost everything except configuration files.
Modified: trunk/packages/hmmer/trunk/debian/patches/debian-changes-3.0-2.1
===================================================================
--- trunk/packages/hmmer/trunk/debian/patches/debian-changes-3.0-2.1 2013-08-15 12:44:25 UTC (rev 14447)
+++ trunk/packages/hmmer/trunk/debian/patches/debian-changes-3.0-2.1 2013-08-15 15:45:50 UTC (rev 14448)
@@ -27,9 +27,9 @@
Reviewed-By: <name and email of someone who approved the patch>
Last-Update: <YYYY-MM-DD>
---- hmmer-3.0.orig/configure
-+++ hmmer-3.0/configure
-@@ -3807,7 +3807,6 @@ if test "$impl_choice" = "none"; then
+--- a/configure
++++ b/configure
+@@ -3849,7 +3849,6 @@
ia64-*-*) impl_choice=sse;;
i?86-*-*) impl_choice=sse;;
x86*-*-*) impl_choice=sse;;
@@ -37,9 +37,9 @@
*) impl_choice=dummy;;
esac
fi
---- hmmer-3.0.orig/configure.ac
-+++ hmmer-3.0/configure.ac
-@@ -300,7 +300,6 @@ if test "$impl_choice" = "none"; then
+--- a/configure.ac
++++ b/configure.ac
+@@ -313,7 +313,6 @@
ia64-*-*) impl_choice=sse;;
i?86-*-*) impl_choice=sse;;
x86*-*-*) impl_choice=sse;;
Added: trunk/packages/hmmer/trunk/debian/patches/fix_clean_target
===================================================================
--- trunk/packages/hmmer/trunk/debian/patches/fix_clean_target (rev 0)
+++ trunk/packages/hmmer/trunk/debian/patches/fix_clean_target 2013-08-15 15:45:50 UTC (rev 14448)
@@ -0,0 +1,44 @@
+--- a/documentation/Makefile.in
++++ b/documentation/Makefile.in
+@@ -24,12 +24,12 @@
+
+ clean:
+ ${QUIET_SUBDIR0}man ${QUIET_SUBDIR1} clean
+- ${QUIET_SUBDIR0}userguide ${QUIET_SUBDIR1} clean
++ ${QUIET_SUBDIR0}userguide ${QUIET_SUBDIR1} clean || true
+ -rm -f *~
+
+ distclean:
+ ${QUIET_SUBDIR0}man ${QUIET_SUBDIR1} distclean
+- ${QUIET_SUBDIR0}userguide ${QUIET_SUBDIR1} distclean
++ ${QUIET_SUBDIR0}userguide ${QUIET_SUBDIR1} distclean || true
+ -rm -f Makefile
+
+ ################################################################
+@@ -43,4 +43,4 @@
+ #
+ # SVN $URL: https://svn.janelia.org/eddylab/eddys/src/hmmer/branches/3.1/documentation/Makefile.in $
+ # SVN $Id: Makefile.in 3649 2011-08-11 15:12:30Z eddys $
+-################################################################
+\ No newline at end of file
++################################################################
+--- a/easel/Makefile.in
++++ b/easel/Makefile.in
+@@ -485,7 +485,7 @@
+ # "make clean" removes almost everything except configuration files
+ #
+ clean:
+- ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean
++ ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean || true
+ ${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} clean
+ ${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} clean
+ -rm -f ${OBJS} libeasel.a
+@@ -502,7 +502,7 @@
+
+
+ distclean: clean
+- ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} distclean
++ ${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} distclean || true
+ ${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} distclean
+ ${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} distclean
+ -rm esl_config.h
Modified: trunk/packages/hmmer/trunk/debian/patches/series
===================================================================
--- trunk/packages/hmmer/trunk/debian/patches/series 2013-08-15 12:44:25 UTC (rev 14447)
+++ trunk/packages/hmmer/trunk/debian/patches/series 2013-08-15 15:45:50 UTC (rev 14448)
@@ -1,2 +1,3 @@
debian-changes-3.0-1
debian-changes-3.0-2.1
+fix_clean_target
Modified: trunk/packages/hmmer/trunk/debian/rules
===================================================================
--- trunk/packages/hmmer/trunk/debian/rules 2013-08-15 12:44:25 UTC (rev 14447)
+++ trunk/packages/hmmer/trunk/debian/rules 2013-08-15 15:45:50 UTC (rev 14448)
@@ -1,24 +1,34 @@
#!/usr/bin/make -f
-include /usr/share/cdbs/1/class/autotools.mk
-include /usr/share/cdbs/1/rules/debhelper.mk
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
-ARCH=`dpkg-architecture -qDEB_BUILD_ARCH_CPU`
+%:
+ dh $@
-ifeq ("amd64",$(ARCH))
-DEB_CONFIGURE_EXTRA_FLAGS := --enable-threads --enable-sse --mandir=$(CURDIR)/debian/tmp/usr/share/man
-else
-ifeq ("powerpc",$(ARCH))
-DEB_CONFIGURE_EXTRA_FLAGS := --enable-threads --enable-vmx --mandir=$(CURDIR)/debian/tmp/usr/share/man
-else
-DEB_CONFIGURE_EXTRA_FLAGS := --enable-threads --mandir=$(CURDIR)/debian/tmp/usr/share/man
+ARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH_CPU)
+
+ifeq (amd64,$(ARCH))
+ DEB_CONFIGURE_EXTRA_FLAGS := --enable-threads --enable-sse
+ else
+ ifeq (powerpc,$(ARCH))
+ DEB_CONFIGURE_EXTRA_FLAGS := --enable-threads --enable-vmx
+ else
+ DEB_CONFIGURE_EXTRA_FLAGS := --enable-threads
+ endif
endif
-endif
-#DEB_CONFIGURE_EXTRA_FLAGS := --enable-threads --enable-mpi
-DEB_MAKE_INSTALL_TARGET := install prefix=$(CURDIR)/debian/tmp/usr
-DEB_MAKE_CHECK_TARGET = check
+override_dh_auto_configure:
+ dh_auto_configure -- $(DEB_CONFIGURE_EXTRA_FLAGS)
-clean::
+override_dh_auto_test:
+ make check
+
+override_dh_auto_clean:
+ dh_auto_clean
rm -f testsuite/esltmp*
rm -f easel/testsuite/esltmp*
+ rm -f tutorial/MADE1.hmm.h3?
+
+override_dh_compress:
+ dh_compress -Xtutorial/
Modified: trunk/packages/hmmer/trunk/debian/watch
===================================================================
--- trunk/packages/hmmer/trunk/debian/watch 2013-08-15 12:44:25 UTC (rev 14447)
+++ trunk/packages/hmmer/trunk/debian/watch 2013-08-15 15:45:50 UTC (rev 14448)
@@ -1,2 +1,2 @@
version=3
-ftp://selab.janelia.org/pub/software/hmmer3/3.0/hmmer-([0-9\.]*)\.tar\.gz
+ftp://selab.janelia.org/pub/software/hmmer3/CURRENT/hmmer-([0-9\.abc]*)\.tar\.gz
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