[med-svn] r5008 - in trunk/packages/hmmer/trunk/debian: . source
Eric Talevich
etal-guest at alioth.debian.org
Thu Jul 8 19:49:12 UTC 2010
Author: etal-guest
Date: 2010-07-08 19:49:11 +0000 (Thu, 08 Jul 2010)
New Revision: 5008
Added:
trunk/packages/hmmer/trunk/debian/hmmer.manpages
trunk/packages/hmmer/trunk/debian/source/
trunk/packages/hmmer/trunk/debian/source/format
Removed:
trunk/packages/hmmer/trunk/debian/hmmer-pvm.1
trunk/packages/hmmer/trunk/debian/hmmer-pvm.README.Debian
trunk/packages/hmmer/trunk/debian/hmmer-pvm.install
trunk/packages/hmmer/trunk/debian/hmmer-pvm.links
trunk/packages/hmmer/trunk/debian/hmmer-pvm.manpages
Modified:
trunk/packages/hmmer/trunk/debian/README.Debian
trunk/packages/hmmer/trunk/debian/changelog
trunk/packages/hmmer/trunk/debian/control
trunk/packages/hmmer/trunk/debian/copyright
trunk/packages/hmmer/trunk/debian/docs
trunk/packages/hmmer/trunk/debian/hmmer.NEWS
trunk/packages/hmmer/trunk/debian/rules
trunk/packages/hmmer/trunk/debian/watch
Log:
Prepared for HMMer version 3.0, without MPI (for now)
Modified: trunk/packages/hmmer/trunk/debian/README.Debian
===================================================================
--- trunk/packages/hmmer/trunk/debian/README.Debian 2010-07-08 19:40:25 UTC (rev 5007)
+++ trunk/packages/hmmer/trunk/debian/README.Debian 2010-07-08 19:49:11 UTC (rev 5008)
@@ -1,15 +1,10 @@
hmmer for Debian
----------------
-This hmmer package has been built with POSIX multithreading support (--enable-threads), Large File Support (--enable-lfs) and Parallel Virtual Machine (--enable-pvm) enabled.
+This is now version 3.0 of HMMER which is real nice
+and should substitute the 2.3 version.
- -- Nelson A. de Oliveira <naoliv at gmail.com> Tue, 08 Aug 2006 23:07:12 -0300
-
-
-Notes on how this pacakge is tested:
-
-The HMMER programs are tested when we assemble our binary packages in our build
-network, using the standard upstream tests. You can consult the results in the
-build logs: ‘http://buildd.debian.org/hmmer’.
-
- -- Charles Plessy <plessy at debian.org> Wed, 16 Dec 2009 13:52:24 +0900
+Support of MPI is now available, even though this
+package does not offer it yet. The PVM of version 2.3
+is no longer supported by upstream and not shipping
+any longer with Debian.
Modified: trunk/packages/hmmer/trunk/debian/changelog
===================================================================
--- trunk/packages/hmmer/trunk/debian/changelog 2010-07-08 19:40:25 UTC (rev 5007)
+++ trunk/packages/hmmer/trunk/debian/changelog 2010-07-08 19:49:11 UTC (rev 5008)
@@ -1,3 +1,9 @@
+hmmer (3.0-1) UNRELEASED; urgency=low
+
+ * The 3.0 release should now substitute the outdated 2.3.x one.
+
+ -- Eric Talevich <etal at uga.edu> Thu, 08 Jul 2010 14:17:59 -0400
+
hmmer (2.3.2-6) UNRELEASED; urgency=low
* Enabled upstream checks in debian/rules.
Modified: trunk/packages/hmmer/trunk/debian/control
===================================================================
--- trunk/packages/hmmer/trunk/debian/control 2010-07-08 19:40:25 UTC (rev 5007)
+++ trunk/packages/hmmer/trunk/debian/control 2010-07-08 19:49:11 UTC (rev 5008)
@@ -1,14 +1,15 @@
Source: hmmer
-Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
+Section: science
Uploaders: Matthew Vernon <matthew at debian.org>,
Nelson A. de Oliveira <naoliv at debian.org>,
Andreas Tille <tille at debian.org>,
- Charles Plessy <plessy at debian.org>
-Build-Depends: cdbs, debhelper (>= 7), pvm-dev, autotools-dev
-Standards-Version: 3.8.3
+ Charles Plessy <plessy at debian.org>,
+ Eric Talevich <etal at uga.edu>
+Build-Depends: cdbs, debhelper (>= 7), autotools-dev
+Standards-Version: 3.9.0
Homepage: http://hmmer.janelia.org/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/hmmer/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/hmmer/trunk/
@@ -16,8 +17,7 @@
Package: hmmer
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: biosquid
-Suggests: hmmer-doc (>= ${source:Version}), hmmer-pvm (>= ${binary:Version})
+Suggests: hmmer-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
@@ -28,22 +28,6 @@
a sequence database to find (and/or align) additional homologues of the
sequence family.
-Package: hmmer-pvm
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, pvm
-Suggests: hmmer-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: hmmer-doc
Section: doc
Architecture: all
Modified: trunk/packages/hmmer/trunk/debian/copyright
===================================================================
--- trunk/packages/hmmer/trunk/debian/copyright 2010-07-08 19:40:25 UTC (rev 5007)
+++ trunk/packages/hmmer/trunk/debian/copyright 2010-07-08 19:49:11 UTC (rev 5008)
@@ -11,9 +11,8 @@
License:
This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
+ it under the terms of the GNU General Public License version 3 as published
+ by the Free Software Foundation.
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
@@ -25,5 +24,5 @@
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
+Public License can be found in `/usr/share/common-licenses/GPL-3'.
Modified: trunk/packages/hmmer/trunk/debian/docs
===================================================================
--- trunk/packages/hmmer/trunk/debian/docs 2010-07-08 19:40:25 UTC (rev 5007)
+++ trunk/packages/hmmer/trunk/debian/docs 2010-07-08 19:49:11 UTC (rev 5008)
@@ -1 +0,0 @@
-NOTES
Deleted: trunk/packages/hmmer/trunk/debian/hmmer-pvm.1
===================================================================
--- trunk/packages/hmmer/trunk/debian/hmmer-pvm.1 2010-07-08 19:40:25 UTC (rev 5007)
+++ trunk/packages/hmmer/trunk/debian/hmmer-pvm.1 2010-07-08 19:49:11 UTC (rev 5008)
@@ -1,19 +0,0 @@
-.TH HMMER-PVM 1 "Tue, 08 Aug 2006 20:00:00 -0300"
-.SH NAME
-hmmer-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 (/usr/share/doc/hmmer-doc/Userguide.pdf.gz), installed with the package "hmmer-doc".
-.PP
-.SH SEE ALSO
-.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).
Deleted: trunk/packages/hmmer/trunk/debian/hmmer-pvm.README.Debian
===================================================================
--- trunk/packages/hmmer/trunk/debian/hmmer-pvm.README.Debian 2010-07-08 19:40:25 UTC (rev 5007)
+++ trunk/packages/hmmer/trunk/debian/hmmer-pvm.README.Debian 2010-07-08 19:49:11 UTC (rev 5008)
@@ -1,8 +0,0 @@
-hmmer-pvm for Debian
---------------------
-
- Please, read the section "Configuring a PVM cluster for HMMER" (page 15)
- at the User's Guide (/usr/share/doc/hmmer-doc/Userguide.pdf.gz), installed with the package "hmmer-doc", 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
Deleted: trunk/packages/hmmer/trunk/debian/hmmer-pvm.install
===================================================================
--- trunk/packages/hmmer/trunk/debian/hmmer-pvm.install 2010-07-08 19:40:25 UTC (rev 5007)
+++ trunk/packages/hmmer/trunk/debian/hmmer-pvm.install 2010-07-08 19:49:11 UTC (rev 5008)
@@ -1,3 +0,0 @@
-debian/tmp/bin/hmmcalibrate-pvm usr/bin
-debian/tmp/bin/hmmpfam-pvm usr/bin
-debian/tmp/bin/hmmsearch-pvm usr/bin
Deleted: trunk/packages/hmmer/trunk/debian/hmmer-pvm.links
===================================================================
--- trunk/packages/hmmer/trunk/debian/hmmer-pvm.links 2010-07-08 19:40:25 UTC (rev 5007)
+++ trunk/packages/hmmer/trunk/debian/hmmer-pvm.links 2010-07-08 19:49:11 UTC (rev 5008)
@@ -1,3 +0,0 @@
-usr/share/man/man1/hmmer-pvm.1.gz usr/share/man/man1/hmmcalibrate-pvm.1.gz
-usr/share/man/man1/hmmer-pvm.1.gz usr/share/man/man1/hmmpfam-pvm.1.gz
-usr/share/man/man1/hmmer-pvm.1.gz usr/share/man/man1/hmmsearch-pvm.1.gz
Deleted: trunk/packages/hmmer/trunk/debian/hmmer-pvm.manpages
===================================================================
--- trunk/packages/hmmer/trunk/debian/hmmer-pvm.manpages 2010-07-08 19:40:25 UTC (rev 5007)
+++ trunk/packages/hmmer/trunk/debian/hmmer-pvm.manpages 2010-07-08 19:49:11 UTC (rev 5008)
@@ -1 +0,0 @@
-debian/hmmer-pvm.1
Modified: trunk/packages/hmmer/trunk/debian/hmmer.NEWS
===================================================================
--- trunk/packages/hmmer/trunk/debian/hmmer.NEWS 2010-07-08 19:40:25 UTC (rev 5007)
+++ trunk/packages/hmmer/trunk/debian/hmmer.NEWS 2010-07-08 19:49:11 UTC (rev 5008)
@@ -1,3 +1,10 @@
+hmmer (3.0-1) unstable; urgency=low
+
+ Transition to 3.0 release, the pvm package is
+ no longer supported.
+
+ -- you <> Thu, 08 Jul 2010 15:06:36 -0400
+
hmmer (2.3.2-3) unstable; urgency=low
Hmmer dependency on biosquid has been downgraded to recommends, as there is
Added: trunk/packages/hmmer/trunk/debian/hmmer.manpages
===================================================================
--- trunk/packages/hmmer/trunk/debian/hmmer.manpages (rev 0)
+++ trunk/packages/hmmer/trunk/debian/hmmer.manpages 2010-07-08 19:49:11 UTC (rev 5008)
@@ -0,0 +1,14 @@
+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/rules
===================================================================
--- trunk/packages/hmmer/trunk/debian/rules 2010-07-08 19:40:25 UTC (rev 5007)
+++ trunk/packages/hmmer/trunk/debian/rules 2010-07-08 19:49:11 UTC (rev 5008)
@@ -3,6 +3,10 @@
include /usr/share/cdbs/1/class/autotools.mk
include /usr/share/cdbs/1/rules/debhelper.mk
-DEB_CONFIGURE_EXTRA_FLAGS := --enable-threads --enable-lfs --enable-pvm
+#DEB_CONFIGURE_EXTRA_FLAGS := --enable-threads --enable-mpi
+DEB_CONFIGURE_EXTRA_FLAGS := --enable-threads --mandir=$(CURDIR)/debian/tmp/usr/share/man
DEB_MAKE_INSTALL_TARGET := install prefix=$(CURDIR)/debian/tmp
DEB_MAKE_CHECK_TARGET = check
+
+clean::
+ rm -f testsuite/esltmp*
Added: trunk/packages/hmmer/trunk/debian/source/format
===================================================================
--- trunk/packages/hmmer/trunk/debian/source/format (rev 0)
+++ trunk/packages/hmmer/trunk/debian/source/format 2010-07-08 19:49:11 UTC (rev 5008)
@@ -0,0 +1 @@
+3.0 (quilt)
Modified: trunk/packages/hmmer/trunk/debian/watch
===================================================================
--- trunk/packages/hmmer/trunk/debian/watch 2010-07-08 19:40:25 UTC (rev 5007)
+++ trunk/packages/hmmer/trunk/debian/watch 2010-07-08 19:49:11 UTC (rev 5008)
@@ -1,2 +1,2 @@
version=3
-ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-([0-9\.]*)\.tar\.gz
+ftp://selab.janelia.org/pub/software/hmmer3/3.0/hmmer-([0-9\.]*)\.tar\.gz
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