[med-svn] [blat] 02/03: Merge together different packaging stuff

[Andreas Tille]

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tille pushed a commit to branch master
in repository blat.

commit d1d0750d44cff554ed724a18d7111d63d61c9ae7
Author: Andreas Tille <tille at debian.org>
Date:   Tue Feb 25 21:39:25 2014 +0100

    Merge together different packaging stuff
---
 debian/clean   |  4 ++++
 debian/control | 41 ++++++++++++++++++++---------------------
 debian/docs    |  1 +
 debian/rules   |  8 +++++---
 4 files changed, 30 insertions(+), 24 deletions(-)

diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..ad18507
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1,4 @@
+blat/test/intron50k/out/*
+blat/test/throwback/test.psl
+blat/test/v29skips/ex1.psl
+webBlat/webBlat
diff --git a/debian/control b/debian/control
index 192f754..1b12d31 100644
--- a/debian/control
+++ b/debian/control
@@ -1,5 +1,5 @@
 Source: blat
-Section: science
+Section: non-free/science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>
@@ -13,26 +13,25 @@ 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.
- The target database of BLAT is not a set of GenBank sequences, but
- instead an index derived from the assembly of the entire genome.
- .
+Description: The BLAST-Like Alignment Tool
  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.
+ similarity of length 25 bases or more. It may miss more divergent or shorter
+ sequence alignments. It will find perfect sequence matches of 25 bases, and
+ sometimes find them down to 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 non-overlapping 11-mers except for those
+ heavily involved in repeats. The index takes up a bit less than a gigabyte of
+ RAM. 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.
  .
- 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.
+ BLAT was written by Jim Kent. Like most of Jim's software, interactive use on
+ this web server is free to all. Sources and executables to run batch jobs on
+ your own server are available free for academic, personal, and non-profit
+ purposes. Non-exclusive commercial licenses are also available.
 
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..e845566
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README
diff --git a/debian/rules b/debian/rules
index 7b7d9af..9a7e095 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,6 +1,6 @@
 #!/usr/bin/make -f
 
-# DH_VERBOSE := 1
+DH_VERBOSE := 1
 
 # some helpful variables - uncomment them if needed
 # shamelessly stolen from http://jmtd.net/log/awk/
@@ -16,7 +16,8 @@ DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
 # 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)
+MACHTYPE := $(shell dpkg-architecture -qDEB_HOST_GNU_CPU)
+DESTDIR  := $(CURDIR)/debian/$(DEBPKGNAME)/usr/
 
 %:
 	dh $@
@@ -26,7 +27,8 @@ override_dh_auto_build:
 	# 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/$(DEBPKGNAME)/usr/ BINDIR=bin/
+	dh_auto_build -- MACHTYPE="$(MACHTYPE)" DESTDIR="$(DESTDIR)" BINDIR=bin/
+	# cd debian/pslCheck; make MACHTYPE="$(MACHTYPE)" DESTDIR="$(DESTDIR)" BINDIR=bin/
 
 #get-orig-source:
 #	. debian/get-orig-source

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