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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> DM-Upload-Allowed: yes +Section: science Uploaders: Matthew Vernon <[email protected]>, Nelson A. de Oliveira <[email protected]>, Andreas Tille <[email protected]>, - Charles Plessy <[email protected]> -Build-Depends: cdbs, debhelper (>= 7), pvm-dev, autotools-dev -Standards-Version: 3.8.3 + Charles Plessy <[email protected]>, + Eric Talevich <[email protected]> +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 <[email protected]>, -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 <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
