[med-svn] r421 - in trunk/packages/infernal/trunk: . debian easel/documentation
smoe-guest at alioth.debian.org
smoe-guest at alioth.debian.org
Tue Sep 11 13:03:17 UTC 2007
Author: smoe-guest
Date: 2007-09-11 13:03:17 +0000 (Tue, 11 Sep 2007)
New Revision: 421
Added:
trunk/packages/infernal/trunk/debian/
trunk/packages/infernal/trunk/debian/README.Debian
trunk/packages/infernal/trunk/debian/changelog
trunk/packages/infernal/trunk/debian/compat
trunk/packages/infernal/trunk/debian/control
trunk/packages/infernal/trunk/debian/copyright
trunk/packages/infernal/trunk/debian/dirs
trunk/packages/infernal/trunk/debian/docs
trunk/packages/infernal/trunk/debian/rules
trunk/packages/infernal/trunk/debian/watch
Modified:
trunk/packages/infernal/trunk/easel/documentation/Makefile
Log:
[svn-inject] Applying Debian modifications to trunk
Property changes on: trunk/packages/infernal/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/infernal/trunk/debian/README.Debian
===================================================================
--- trunk/packages/infernal/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/infernal/trunk/debian/README.Debian 2007-09-11 13:03:17 UTC (rev 421)
@@ -0,0 +1,14 @@
+infernal for Debian
+-------------------
+
+The source of the user guide (downloadable at
+ftp://infernal.janelia.org/pub/software/infernal/Userguide.pdf) is
+apparently not distributed with the source of the program.
+
+The programmer's handbook is available from the source
+but was not compiled for the Debian package.
+The packaging will become part of the Debian-Med
+Custom Debian Distribution and thus invivites any
+interested party to join in for maintaining it.
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 10 Sep 2007 23:15:37 +0200
Added: trunk/packages/infernal/trunk/debian/changelog
===================================================================
--- trunk/packages/infernal/trunk/debian/changelog (rev 0)
+++ trunk/packages/infernal/trunk/debian/changelog 2007-09-11 13:03:17 UTC (rev 421)
@@ -0,0 +1,6 @@
+infernal (0.81-1) unstable; urgency=low
+
+ * Initial release (Closes: #441840)
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 10 Sep 2007 23:15:37 +0200
+
Added: trunk/packages/infernal/trunk/debian/compat
===================================================================
--- trunk/packages/infernal/trunk/debian/compat (rev 0)
+++ trunk/packages/infernal/trunk/debian/compat 2007-09-11 13:03:17 UTC (rev 421)
@@ -0,0 +1 @@
+5
Added: trunk/packages/infernal/trunk/debian/control
===================================================================
--- trunk/packages/infernal/trunk/debian/control (rev 0)
+++ trunk/packages/infernal/trunk/debian/control 2007-09-11 13:03:17 UTC (rev 421)
@@ -0,0 +1,23 @@
+Source: infernal
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 5)
+Standards-Version: 3.7.2
+
+Package: infernal
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: RNA sequence comparison
+ Infernal ("INFERence of RNA ALignment") is for searching DNA sequence
+ databases for RNA structure and sequence similarities. It is an
+ implementation of a special case of profile stochastic context-free
+ grammars called covariance models (CMs). A CM is like a sequence
+ profile, but it scores a combination of sequence consensus and RNA
+ secondary structure consensus, so in many cases, it is more capable of
+ identifying RNA homologs that conserve their secondary structure more
+ than their primary sequence.
+ .
+ The tool is an integral component of the Rfam database.
+ .
+ http://infernal.janelia.org/
Added: trunk/packages/infernal/trunk/debian/copyright
===================================================================
--- trunk/packages/infernal/trunk/debian/copyright (rev 0)
+++ trunk/packages/infernal/trunk/debian/copyright 2007-09-11 13:03:17 UTC (rev 421)
@@ -0,0 +1,46 @@
+This package was debianized by Steffen Moeller <moeller at debian.org> on
+Mon, 10 Sep 2007 23:15:37 +0200.
+
+It was downloaded from ftp://infernal.janelia.org/pub/software/infernal
+
+Upstream Author(s):
+
+
+ Infernal developer team at HHMI Janelia Farm:
+ Diana Kolbe <kolbed at janelia.hhmi.org>
+ Eric Nawrocki <nawrockie at janelia.hhmi.org>
+ Sean Eddy <eddy at janelia.hhmi.org>.
+
+ The "rigfilters" code was contributed by Zasha Weinberg and Larry
+ Ruzzo, University of Washington Seattle.
+
+Copyright:
+
+ <Copyright (C) YYYY Name OfAuthor>
+ <likewise for another author>
+
+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.
+
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ 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'.
+
+The Debian packaging is (C) 2007, Steffen Moeller <moeller at debian.org> and
+is licensed under the GPL, see above.
+
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
Added: trunk/packages/infernal/trunk/debian/dirs
===================================================================
--- trunk/packages/infernal/trunk/debian/dirs (rev 0)
+++ trunk/packages/infernal/trunk/debian/dirs 2007-09-11 13:03:17 UTC (rev 421)
@@ -0,0 +1 @@
+usr/bin
Added: trunk/packages/infernal/trunk/debian/docs
===================================================================
--- trunk/packages/infernal/trunk/debian/docs (rev 0)
+++ trunk/packages/infernal/trunk/debian/docs 2007-09-11 13:03:17 UTC (rev 421)
@@ -0,0 +1,2 @@
+00README
+00README-MPI
Added: trunk/packages/infernal/trunk/debian/rules
===================================================================
--- trunk/packages/infernal/trunk/debian/rules (rev 0)
+++ trunk/packages/infernal/trunk/debian/rules 2007-09-11 13:03:17 UTC (rev 421)
@@ -0,0 +1,130 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+#
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+#
+# Modified to make a template file for a multi-binary package with separated
+# build-arch and build-indep targets by Bill Allombert 2001
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+# This has to be exported to make some magic below work.
+export DH_OPTIONS
+
+# These are used for cross-compiling and for saving the configure script
+# from having to guess our platform (since we know it already)
+DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
+DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+config.status: configure
+ dh_testdir
+ # Add here commands to configure the package.
+ifneq "$(wildcard /usr/share/misc/config.sub)" ""
+ cp -f /usr/share/misc/config.sub config.sub
+endif
+ifneq "$(wildcard /usr/share/misc/config.guess)" ""
+ cp -f /usr/share/misc/config.guess config.guess
+endif
+ ./configure --host=$(DEB_HOST_GNU_TYPE) --build=$(DEB_BUILD_GNU_TYPE) --prefix=/usr --pdfdir=\$${prefix}/share/doc/infernal --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info CFLAGS="$(CFLAGS)" LDFLAGS="-Wl,-z,defs"
+
+
+#Architecture
+build: build-arch build-indep
+
+build-arch: build-arch-stamp
+build-arch-stamp: config.status
+
+ # Add here commands to compile the arch part of the package.
+ $(MAKE)
+ touch $@
+
+build-indep: build-indep-stamp
+build-indep-stamp: config.status
+ # Add here commands to compile the indep part of the package.
+ #$(MAKE) doc
+ touch $@
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-arch-stamp build-indep-stamp #CONFIGURE-STAMP#
+ # Add here commands to clean up after the build process.
+ -$(MAKE) distclean
+ rm -f config.sub config.guess
+ dh_clean cm*.1 */*.log *.log */Makefile Makefile
+
+install: install-indep install-arch
+install-indep:
+ #dh_testdir
+ #dh_testroot
+ #dh_clean -k -i
+ #dh_installdirs -i
+ # Add here commands to install the indep part of the package into
+ # debian/<package>-doc.
+ #INSTALLDOC#
+ #dh_install -i
+
+cm2hmm.1:
+ for i in documentation/manpages/*.man ; \
+ do \
+ m=`basename $$i .man`.1 ; \
+ cp $$i $$m; \
+ done
+
+install-arch: cm2hmm.1
+ dh_testdir
+ dh_testroot
+ dh_clean -k -s
+ dh_installdirs -s
+
+ # Add here commands to install the arch part of the package into
+ # debian/tmp.
+ $(MAKE) prefix=$(CURDIR)/debian/infernal/usr install
+
+ dh_install -s
+# Must not depend on anything. This is to be called by
+# binary-arch/binary-indep
+# in another 'make' thread.
+binary-common:
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installexamples intro
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+# dh_perl
+ dh_makeshlibs
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+# Build architecture independant packages using the common target.
+binary-indep: build-indep install-indep
+ #$(MAKE) -f debian/rules DH_OPTIONS=-i binary-common
+
+# Build architecture dependant packages using the common target.
+binary-arch: build-arch install-arch
+ $(MAKE) -f debian/rules DH_OPTIONS=-s binary-common
+
+binary: binary-arch
+.PHONY: build clean binary-indep binary-arch binary install install-indep install-arch
Property changes on: trunk/packages/infernal/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/infernal/trunk/debian/watch
===================================================================
--- trunk/packages/infernal/trunk/debian/watch (rev 0)
+++ trunk/packages/infernal/trunk/debian/watch 2007-09-11 13:03:17 UTC (rev 421)
@@ -0,0 +1,4 @@
+version=3
+ftp://infernal.janelia.org/pub/software/infernal/infernal-(.*)\.tar\.gz debian uupdate
+
+
Modified: trunk/packages/infernal/trunk/easel/documentation/Makefile
===================================================================
--- trunk/packages/infernal/trunk/easel/documentation/Makefile 2007-09-11 13:03:00 UTC (rev 420)
+++ trunk/packages/infernal/trunk/easel/documentation/Makefile 2007-09-11 13:03:17 UTC (rev 421)
@@ -64,7 +64,7 @@
autodoc:
mkdir -p autotext
for module in ${MODULES}; do\
- ./autodoc_functions ../$$module.c > autotext/$${module}_functions.tex;\
+ perl ./autodoc_functions ../$$module.c > autotext/$${module}_functions.tex;\
done
cexcerpt:
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