[med-svn] r4032 - trunk/packages/infernal/trunk/debian
Steffen Moeller
steffen_moeller at gmx.de
Sat Sep 26 17:02:59 UTC 2009
Hi Andreas,
please add them (from
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2677745):
Motivation: Accuracy of automated structural RNA alignment is improved by using
models that consider not only primary sequence but also secondary structure
information. However, current RNA structural alignment approaches tend to
perform poorly on incomplete sequence fragments, such as single reads from
metagenomic environmental surveys, because nucleotides that are expected to be
base paired are missing.
Results: We present a local RNA structural alignment algorithm, trCYK, for
aligning and scoring incomplete sequences under a model using primary sequence
conservation and secondary structure information when possible. The trCYK
algorithm improves alignment accuracy and coverage of sequence fragments of
structural RNAs in simulated metagenomic shotgun datasets.
Availability: The source code for Infernal 1.0, which includes trCYK, is
available at http://infernal.janelia.org
Cheers,
Steffen
Andreas Tille wrote:
> Author: tille
> Date: 2009-09-26 07:50:40 +0000 (Sat, 26 Sep 2009)
> New Revision: 4032
>
> Added:
> trunk/packages/infernal/trunk/debian/infernal.install
> Modified:
> trunk/packages/infernal/trunk/debian/changelog
> trunk/packages/infernal/trunk/debian/rules
> Log:
> Rewritten debian/rules to short dh version; install src/{trcyk,truncyk_check} to /usr/bin - Steffen, could you please comment on this whether leaving these binaries out or are they new?
>
>
> Modified: trunk/packages/infernal/trunk/debian/changelog
> ===================================================================
> --- trunk/packages/infernal/trunk/debian/changelog 2009-09-26 07:05:38 UTC (rev 4031)
> +++ trunk/packages/infernal/trunk/debian/changelog 2009-09-26 07:50:40 UTC (rev 4032)
> @@ -11,7 +11,7 @@
> - s/Debian-Med/Debian Med/
> - Build-Depends: debhelper (>= 7.1) autotools-dev
> - Package: infernal-doc
> - * debian/rules: removed deprecated -k option from dh_clean
> + * debian/rules rewritten to make use of short dh
> * debian/copyright:
> - added myself to Copyright holders of debian/*
> - squid is not part of the upstream tarball anymore so this
> @@ -19,6 +19,8 @@
> - files/Userguide.pdf: Copied comment about PDF = source from
> README.Debian
> * debian/infernal-doc.doc-base
> + * debian/infernal.install: install src/{trcyk,truncyk_check} to
> + /usr/bin
>
> -- Andreas Tille <tille at debian.org> Fri, 25 Sep 2009 15:17:22 +0200
>
>
> Added: trunk/packages/infernal/trunk/debian/infernal.install
> ===================================================================
> --- trunk/packages/infernal/trunk/debian/infernal.install (rev 0)
> +++ trunk/packages/infernal/trunk/debian/infernal.install 2009-09-26 07:50:40 UTC (rev 4032)
> @@ -0,0 +1,3 @@
> +src/trcyk usr/bin
> +src/truncyk_check usr/bin
> +
>
> Modified: trunk/packages/infernal/trunk/debian/rules
> ===================================================================
> --- trunk/packages/infernal/trunk/debian/rules 2009-09-26 07:05:38 UTC (rev 4031)
> +++ trunk/packages/infernal/trunk/debian/rules 2009-09-26 07:50:40 UTC (rev 4032)
> @@ -1,146 +1,17 @@
> #!/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
> +%:
> + dh $@
>
> -# 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.
> +override_dh_auto_clean:
> if [ -r Makefile ]; then $(MAKE) distclean; fi
> - rm -f config.sub config.guess
> - dh_clean cm*.1 */*.log *.log */Makefile Makefile documentation/manpages/*.1
> + dh_clean *.1 */*.log *.log */Makefile Makefile documentation/manpages/*.1
>
> -install: install-indep install-arch
> -install-indep:
> - #dh_testdir
> - #dh_testroot
> - #dh_clean -i
> - #dh_installdirs -i
> - # Add here commands to install the indep part of the package into
> - # debian/<package>-doc.
> - #INSTALLDOC#
> - #dh_install -i
> +override_dh_auto_install:
> + $(MAKE) install PREFIX=`pwd`/debian/tmp
>
> -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 -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 *.1
> - 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
> -
> get-orig-source:
> - VERSION=`head -1 debian/changelog | cut -f1 -d- | cut -f2 -d\( | tr -d '\n'` ; \
> - URL="ftp://selab.janelia.org/pub/software/infernal/infernal.tar.gz"; \
> - cd ..; \
> - wget -nc $$URL && tar xzvf infernal.tar.gz; \
> - p=`pwd`; \
> - if [ -d infernal-$$VERSION ]; then \
> - cd infernal-$$VERSION && rm -rf ./easel/documentation Userguide.pdf ; \
> - else \
> - echo "Please check debian/changelog, the version you have downloaded is apparently newer than expected." ; \
> - exit -1 ; \
> - fi; \
> - cd $$p ; \
> - tar czvf infernal_$${VERSION}.orig.tar.gz infernal-$$VERSION && rm -rf infernal-$$VERSION
> -
> -
> -binary: binary-arch
> -.PHONY: build clean binary-indep binary-arch binary install install-indep install-arch
> + VERSION=`dpkg-parsechangelog | grep Ver | cut -d' ' -f2 | cut -d- -f1` ; \
> + URL="ftp://selab.janelia.org/pub/software/infernal/infernal-$${VERSION}.tar.gz"; \
> + ln -s infernal-$${VERSION}.tar.gz infernal_$${VERSION}.orig.tar.gz
>
>
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