Andreas Tille pushed to branch master at Debian Med / hmmer2
Commits: 1a1e497d by Andreas Tille at 2019-01-11T18:09:43Z Drop hmmer2-pvm package - - - - - e0bfa4d0 by Andreas Tille at 2019-01-11T18:10:02Z Fix install path - - - - - a0d40a61 by Andreas Tille at 2019-01-11T18:22:17Z Fix names - - - - - 1b03ee93 by Andreas Tille at 2019-01-11T18:23:39Z libhmmer2-dev package drops static lib - - - - - 8b923271 by Andreas Tille at 2019-01-11T18:24:36Z Fix doc installation - - - - - e8e828b1 by Andreas Tille at 2019-01-11T18:28:44Z No upstream changelog - - - - - 13 changed files: - debian/changelog - debian/control - − debian/docs - − debian/hmmer2-pvm.1 - − debian/hmmer2-pvm.README.Debian - − debian/hmmer2-pvm.install - − debian/hmmer2-pvm.links - − debian/hmmer2-pvm.manpages - + debian/hmmer2.docs - debian/libhmmer2-dev.install - + debian/patches/fix_install.patch - debian/patches/series - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -7,6 +7,9 @@ hmmer2 (2.5j+dfsg-1) UNRELEASED; urgency=medium * New upstream version * debhelper 12 * Standards-Version: 4.3.0 + * Drop hmmer2-pvm package + * libhmmer2-dev package drops static lib (this is not automatically + generated by upstream any more) -- Andreas Tille <[email protected]> Fri, 11 Jan 2019 15:43:07 +0100 ===================================== debian/control ===================================== @@ -21,8 +21,7 @@ Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Recommends: biosquid -Suggests: hmmer2-doc (>= ${source:Version}), - hmmer2-pvm (>= ${binary:Version}) +Suggests: hmmer2-doc (>= ${source:Version}) Description: profile hidden Markov models for protein sequence analysis HMMER is an implementation of profile hidden Markov model methods for sensitive searches of biological sequence databases using multiple sequence @@ -33,24 +32,6 @@ Description: profile hidden Markov models for protein sequence analysis a sequence database to find (and/or align) additional homologues of the sequence family. -Package: hmmer2-pvm -Architecture: any -Depends: ${shlibs:Depends}, - ${misc:Depends}, - pvm -Suggests: hmmer2-doc (>= ${binary:Version}) -Description: HMMER programs with PVM (Parallel Virtual Machine) support - HMMER is an implementation of profile hidden Markov model methods for - sensitive searches of biological sequence databases using multiple sequence - alignments as queries. - . - Given a multiple sequence alignment as input, HMMER builds a statistical - model called a "hidden Markov model" which can then be used as a query into - a sequence database to find (and/or align) additional homologues of the - sequence family. - . - This package contains HMMER programs compiled with PVM support. - Package: hmmer2-doc Architecture: all Section: doc ===================================== debian/docs deleted ===================================== @@ -1 +0,0 @@ -NOTES ===================================== debian/hmmer2-pvm.1 deleted ===================================== @@ -1,20 +0,0 @@ -.TH HMMER-PVM 1 "Tue, 08 Aug 2006 20:00:00 -0300" -.SH NAME -hmmer2-pvm \- HMMER utilities for PVM clusters -.SH DESCRIPTION -Information on how to use the programs -.B hmmcalibrate-pvm -, -.B hmmpfam-pvm -and -.B hmmsearch-pvm -is available on the section "Configuring a PVM cluster for HMMER" (page 15) at the User's Guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf). -.PP -.SH SEE ALSO -.BR hmmer2 (1), -.BR hmmer (1) -.SH AUTHOR -HMMER was written by Sean Eddy. -.PP -This manual page was written by Nelson A. de Oliveira <[email protected]>, -for the Debian project (but may be used by others). ===================================== debian/hmmer2-pvm.README.Debian deleted ===================================== @@ -1,8 +0,0 @@ -hmmer2-pvm for Debian --------------------- - - Please, read the section "Configuring a PVM cluster for HMMER" (page 15) - at the User's Guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf), to see how to configure properly Hmmer on a PVM - cluster. - - -- Nelson A. de Oliveira <[email protected]> Tue, 08 Aug 2006 23:07:12 -0300 ===================================== debian/hmmer2-pvm.install deleted ===================================== @@ -1,3 +0,0 @@ -debian/tmp/bin/hmm2calibrate-pvm usr/bin -debian/tmp/bin/hmm2pfam-pvm usr/bin -debian/tmp/bin/hmm2search-pvm usr/bin ===================================== debian/hmmer2-pvm.links deleted ===================================== @@ -1,3 +0,0 @@ -usr/share/man/man1/hmmer2-pvm.1.gz usr/share/man/man1/hmm2calibrate-pvm.1.gz -usr/share/man/man1/hmmer2-pvm.1.gz usr/share/man/man1/hmm2pfam-pvm.1.gz -usr/share/man/man1/hmmer2-pvm.1.gz usr/share/man/man1/hmm2search-pvm.1.gz ===================================== debian/hmmer2-pvm.manpages deleted ===================================== @@ -1 +0,0 @@ -debian/hmmer2-pvm.1 ===================================== debian/hmmer2.docs ===================================== @@ -0,0 +1 @@ +Release-Notes ===================================== debian/libhmmer2-dev.install ===================================== @@ -4,5 +4,5 @@ src/funcs.h usr/include/hmmer2 src/globals.h usr/include/hmmer2 src/postprob.h usr/include/hmmer2 src/structs.h usr/include/hmmer2 -src/libhmmer.a usr/lib/${DEB_HOST_MULTIARCH} +#src/libhmmer.a usr/lib/${DEB_HOST_MULTIARCH} debian/pkgconfig usr/lib/${DEB_HOST_MULTIARCH} ===================================== debian/patches/fix_install.patch ===================================== @@ -0,0 +1,23 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Fri, 11 Jan 2019 15:43:07 +0100 +Description: Do not duplicate prefix + +--- a/Makefile ++++ b/Makefile +@@ -55,13 +55,13 @@ src/libhmmer.a: + # Prefix those paths with ${DESTDIR} (rarely used, usually null; + # may be set on a make command line when building contrib RPMs). + install: +- mkdir -p ${DESTDIR}/$(BINDIR)/ ++ mkdir -p $(BINDIR) + + for file in $(PROGS) ; do\ +- cp src/$$file "${DESTDIR}/$(BINDIR)/$$file""$(PROGSUFFIX)" ;\ ++ cp src/$$file "$(BINDIR)/$$file""$(PROGSUFFIX)" ;\ + done + for file in hmmer2 $(ls documentation/man/); do\ +- install -D documentation/man/$$file.man ${DESTDIR}/$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ ++ install -D documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ + done + + # Reverses the steps of "make install". However, this should be handled ===================================== debian/patches/series ===================================== @@ -1,3 +1,4 @@ use_debian_packaged_biosquid.patch build_libhmmer.a_with-fPIC.patch fix_typo.patch +fix_install.patch ===================================== debian/rules ===================================== @@ -30,16 +30,13 @@ override_dh_auto_configure: override_dh_auto_install: dh_auto_install -- prefix=$(CURDIR)/debian/tmp # lkajan: rename binaries and man pages like this: s/hmm/hmm2/ - except hmmer.1, rename that to hmmer2.1: - rename 's/^hmm/hmm2/;' $(CURDIR)/debian/tmp/bin/* - cd $(CURDIR)/debian/tmp/bin; rename 's/^hmm/hmm2/;' * - cd $(CURDIR)/debian/tmp/share/man/man1; rename 's/^hmm/hmm2/;' * - mv $(CURDIR)/debian/tmp/share/man/man1/hmm2er.1 $(CURDIR)/debian/tmp/share/man/man1/hmmer2.1 + rename 's/^hmm(.+)2/hmm2$$1/;' $(CURDIR)/debian/tmp/bin/* + cd $(CURDIR)/debian/tmp/bin; rename 's/^hmm(.+)2/hmm2$$1/;' * + cd $(CURDIR)/debian/tmp/share/man/man1; rename 's/^hmm(.+)2/hmm2$$1/;' * + # mv $(CURDIR)/debian/tmp/share/man/man1/hmm2er.1 $(CURDIR)/debian/tmp/share/man/man1/hmmer2.1 # lkajan: resolve man page hypen issue: sed -i -e 's/--/\\-\\-/g;s/-\([[:alpha:]]\)\b/\\-\1/g;' $(CURDIR)/debian/tmp/share/man/man1/* -override_dh_installchangelogs: - dh_installchangelogs -k 00README - override_dh_installexamples: dh_installexamples mkdir -p $(sampledir); View it on GitLab: https://salsa.debian.org/med-team/hmmer2/compare/60ca6f1a26e348b0d52949c46367ea159f54f080...e8e828b135bc5fd7855253eea5e3ac3deb680306 -- View it on GitLab: https://salsa.debian.org/med-team/hmmer2/compare/60ca6f1a26e348b0d52949c46367ea159f54f080...e8e828b135bc5fd7855253eea5e3ac3deb680306 You're receiving this email because of your account on salsa.debian.org.
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