[med-svn] [Git][med-team/hmmer2][master] 6 commits: Drop hmmer2-pvm package
Andreas Tille
gitlab at salsa.debian.org
Fri Jan 11 18:35:13 GMT 2019
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 <tille at debian.org> 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 <naoliv at gmail.com>,
-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 <naoliv at gmail.com> 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 <tille at debian.org>
+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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190111/faf3880d/attachment-0001.html>
More information about the debian-med-commit
mailing list