[med-svn] [blat] 02/02: Add initial debian/ dir

Thu Feb 20 18:54:23 UTC 2014

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tille pushed a commit to branch master
in repository blat.

commit 3277733ea9b7783958fe0380e856cff854072e66
Author: Andreas Tille <tille at debian.org>
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 <tille at debian.org>  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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+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 <tille at debian.org>
+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

-- 
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