This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository blat.
commit 3277733ea9b7783958fe0380e856cff854072e66 Author: Andreas Tille <[email protected]> Date: Thu Feb 20 19:52:53 2014 +0100 Add initial debian/ dir --- debian/changelog | 5 +++++ debian/compat | 1 + debian/control | 37 +++++++++++++++++++++++++++++++++++++ debian/copyright | 16 ++++++++++++++++ debian/dirs | 1 + debian/rules | 32 ++++++++++++++++++++++++++++++++ debian/source/format | 1 + debian/watch | 2 ++ 8 files changed, 95 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..0ccf728 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +blat (35-1) UNRELEASED; urgency=low + + * Initial release (Closes: #<bug>) + + -- Andreas Tille <[email protected]> Thu, 20 Feb 2014 11:14:17 +0100 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..ec63514 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +9 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..7c024b5 --- /dev/null +++ b/debian/control @@ -0,0 +1,37 @@ +Source: blat +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 9) +Standards-Version: 3.9.5 +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/blat/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/blat/trunk/ +Homepage: http://genome.ucsc.edu/cgi-bin/hgBlat + +Package: blat +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: BLAST-like Alignment Tool + Blat is an alignment tool like BLAST, but it is structured differently. + he target database of BLAT is not a set of GenBank sequences, but + instead an index derived from the assembly of the entire genome. + . + BLAT on DNA is designed to quickly find sequences of 95% and greater + similarity of length 25 bases or more. It may miss more divergent or + shorter sequence alignments. It will find perfect sequence matches of 20 + bases. BLAT on proteins finds sequences of 80% and greater similarity of + length 20 amino acids or more. In practice DNA BLAT works well on + primates, and protein blat on land vertebrates. + . + BLAT is not BLAST. DNA BLAT works by keeping an index of the entire + genome in memory. The index consists of all overlapping 11-mers stepping + by 5 except for those heavily involved in repeats. The index takes up + about 2 gigabytes of RAM. RAM can be further reduced to less than 1 GB + by increasing step size to 11. The genome itself is not kept in memory, + allowing BLAT to deliver high performance on a reasonably priced Linux + box. The index is used to find areas of probable homology, which are + then loaded into memory for a detailed alignment. Protein BLAT works in + a similar manner, except with 4-mers rather than 11-mers. The protein + index takes a little more than 2 gigabytes. + diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..77ea13a --- /dev/null +++ b/debian/copyright @@ -0,0 +1,16 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: <pkg> +Source: <path_to_download> +Files-Excluded: + CVS + */CVS + */*/CVS + */*/*/CVS + +Files: * +Copyright: © 20xx-20yy <upstream> +License: <license> + +Files: debian/* +Copyright: © 2012 Andreas Tille <[email protected]> +License: <license> diff --git a/debian/dirs b/debian/dirs new file mode 100644 index 0000000..e772481 --- /dev/null +++ b/debian/dirs @@ -0,0 +1 @@ +usr/bin diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..7b7d9af --- /dev/null +++ b/debian/rules @@ -0,0 +1,32 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +# some helpful variables - uncomment them if needed +# shamelessly stolen from http://jmtd.net/log/awk/ +#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}') +#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//') +#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}') +DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') +#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf) +#GIT_TAG := $(subst ~,_,$(VERSION)) + +# alternatively to manually set those variables you can +# include /usr/share/cdbs/1/rules/buildvars.mk +# and use what is set there. Any hint whether dh might set variables in +# a similar manner are welcome. + +MACHTYPE := $(shell dpkg-architecture -qDEB_BUILD_ARCH) + +%: + dh $@ + +override_dh_auto_build: + # upstream makefile does all in one ... waiting until dh_installdirs has done its work + # FIXME: That's a bit hackish and it seems to be more sane to fix the makefile + +override_dh_auto_install: + dh_auto_build -- MACHTYPE="$(MACHTYPE)" DESTDIR=$(CURDIR)/debian/$(DEBPKGNAME)/usr/ BINDIR=bin/ + +#get-orig-source: +# . debian/get-orig-source diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..1d51de4 --- /dev/null +++ b/debian/watch @@ -0,0 +1,2 @@ +version=3 +http://users.soe.ucsc.edu/~kent/src/ blatSrc([\d]+)\.zip -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/blat.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
