[med-svn] r2479 - in trunk/packages/last-align/trunk: . debian src
plessy at alioth.debian.org
plessy at alioth.debian.org
Thu Sep 11 06:56:58 UTC 2008
Author: plessy
Date: 2008-09-11 06:56:57 +0000 (Thu, 11 Sep 2008)
New Revision: 2479
Added:
trunk/packages/last-align/trunk/debian/
trunk/packages/last-align/trunk/debian/README.Debian
trunk/packages/last-align/trunk/debian/README.source
trunk/packages/last-align/trunk/debian/changelog
trunk/packages/last-align/trunk/debian/compat
trunk/packages/last-align/trunk/debian/control
trunk/packages/last-align/trunk/debian/copyright
trunk/packages/last-align/trunk/debian/docs
trunk/packages/last-align/trunk/debian/install
trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-evalues
trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-manual
trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-scripts
trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-seeds
trunk/packages/last-align/trunk/debian/rules
trunk/packages/last-align/trunk/debian/watch
Modified:
trunk/packages/last-align/trunk/src/Alignment.cc
trunk/packages/last-align/trunk/src/AlignmentPot.hh
trunk/packages/last-align/trunk/src/Alphabet.cc
trunk/packages/last-align/trunk/src/MultiSequence.cc
trunk/packages/last-align/trunk/src/PeriodicSpacedSeed.cc
trunk/packages/last-align/trunk/src/ScoreMatrix.cc
trunk/packages/last-align/trunk/src/ScoreMatrix.hh
trunk/packages/last-align/trunk/src/SuffixArray.hh
trunk/packages/last-align/trunk/src/XdropAligner.hh
trunk/packages/last-align/trunk/src/lastal.cc
trunk/packages/last-align/trunk/src/lastdb.cc
Log:
[svn-inject] Applying Debian modifications to trunk
Property changes on: trunk/packages/last-align/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/last-align/trunk/debian/README.Debian
===================================================================
--- trunk/packages/last-align/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/last-align/trunk/debian/README.Debian 2008-09-11 06:56:57 UTC (rev 2479)
@@ -0,0 +1,6 @@
+last-align for Debian
+---------------------
+
+<possible notes regarding this package - if none, delete this file>
+
+ -- Charles Plessy <plessy at debian.org> Wed, 10 Sep 2008 19:49:11 +0900
Added: trunk/packages/last-align/trunk/debian/README.source
===================================================================
--- trunk/packages/last-align/trunk/debian/README.source (rev 0)
+++ trunk/packages/last-align/trunk/debian/README.source 2008-09-11 06:56:57 UTC (rev 2479)
@@ -0,0 +1,9 @@
+This package is maintained by the Debian Med packagign team. Please refer to
+our group policy if you would like to commit to our Subversion repository. All
+Debian developpers have write acces to it.
+
+http://debian-med.alioth.debian.org/docs/policy.html
+
+Upstream sources are distributed as a ZIP archive. The debian/rules file
+contains a rule named `get-orig-source' to create a gzipped tar archive whose
+name follows the Debian policy.
Added: trunk/packages/last-align/trunk/debian/changelog
===================================================================
--- trunk/packages/last-align/trunk/debian/changelog (rev 0)
+++ trunk/packages/last-align/trunk/debian/changelog 2008-09-11 06:56:57 UTC (rev 2479)
@@ -0,0 +1,6 @@
+last-align (7-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Charles Plessy <plessy at debian.org> Wed, 10 Sep 2008 19:49:11 +0900
+
Added: trunk/packages/last-align/trunk/debian/compat
===================================================================
--- trunk/packages/last-align/trunk/debian/compat (rev 0)
+++ trunk/packages/last-align/trunk/debian/compat 2008-09-11 06:56:57 UTC (rev 2479)
@@ -0,0 +1 @@
+7
Added: trunk/packages/last-align/trunk/debian/control
===================================================================
--- trunk/packages/last-align/trunk/debian/control (rev 0)
+++ trunk/packages/last-align/trunk/debian/control 2008-09-11 06:56:57 UTC (rev 2479)
@@ -0,0 +1,30 @@
+Source: last-align
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy at debian.org>
+Build-Depends: debhelper (>= 7), cdbs
+Standards-Version: 3.8.0
+Homepage: http://last.cbrc.jp/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/last-align/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/last-align/trunk/
+
+Package: last-align
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: python
+Description: genome-scale comparison of biological sequences.
+ LAST is software for comparing and aligning sequences, typically DNA or
+ protein sequences. LAST is similar to BLAST, but it copes better with very
+ large amounts of sequence data. Here are two things LAST is good at:
+ .
+ * Comparing large (e.g. mammalian) genomes.
+ * Mapping lots of sequence tags onto a genome.
+ .
+ The main technical innovation is that LAST finds initial matches based on
+ their multiplicity, instead of using a fixed size (e.g. BLAST uses 11-mers).
+ This allows us to map tags to genomes without repeat-masking, without becoming
+ overwhelmed by repetitive hits. To find these variable-sized matches, it uses
+ a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a
+ discontiguous suffix array, analogous to spaced seeds.
Added: trunk/packages/last-align/trunk/debian/copyright
===================================================================
--- trunk/packages/last-align/trunk/debian/copyright (rev 0)
+++ trunk/packages/last-align/trunk/debian/copyright 2008-09-11 06:56:57 UTC (rev 2479)
@@ -0,0 +1,28 @@
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+Upstream-Author: Martin C. Frith and Paul B. Horton <last at cbrc.jp>
+Packaged-By: Charles Plessy <plessy at debian.org>
+Packaged-Date: Wed, 10 Sep 2008 19:49:11 +0900.
+Upstream-Source: http://last.cbrc.jp/archive/last-7.zip
+
+Files: *
+Copyright: © 2008
+License: GPL-3+
+ This program 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 3 of the License, or
+ (at your option) any later version.
+ .
+ This program 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 program. If not, see <http://www.gnu.org/licenses/>.
+X-Comment: On Debian systems the full text of the GNU General Public License
+ can be found in the `/usr/share/common-licenses/GPL' file.
+
+Files: debian/*
+Copyright: © 2008, Charles Plessy <plessy at debian.org>
+License: Same as LAST itself
+ See above.
Added: trunk/packages/last-align/trunk/debian/docs
===================================================================
--- trunk/packages/last-align/trunk/debian/docs (rev 0)
+++ trunk/packages/last-align/trunk/debian/docs 2008-09-11 06:56:57 UTC (rev 2479)
@@ -0,0 +1,2 @@
+ChangeLog.txt
+doc/*
Added: trunk/packages/last-align/trunk/debian/install
===================================================================
--- trunk/packages/last-align/trunk/debian/install (rev 0)
+++ trunk/packages/last-align/trunk/debian/install 2008-09-11 06:56:57 UTC (rev 2479)
@@ -0,0 +1,3 @@
+scripts/* usr/bin
+src/lastal usr/bin
+src/lastdb usr/bin
Added: trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-evalues
===================================================================
--- trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-evalues (rev 0)
+++ trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-evalues 2008-09-11 06:56:57 UTC (rev 2479)
@@ -0,0 +1,9 @@
+Document: last-align-evalues
+Title: LAST manual: e-values
+Author: Martin C. Frith and Paul B. Horton
+Abstract: The following tables indicate how many high-scoring alignments are
+ expected, on average, between a pair of completely random sequences.
+Section: Science/Biology
+
+Format: text
+Files: /usr/share/doc/last-align/evalue-tables.txt.gz
Added: trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-manual
===================================================================
--- trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-manual (rev 0)
+++ trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-manual 2008-09-11 06:56:57 UTC (rev 2479)
@@ -0,0 +1,8 @@
+Document: last-align-manual
+Title: LAST manual: main section.
+Author: Martin C. Frith and Paul B. Horton
+Abstract: This manual describes how to use the LAST genome-scale alignment program.
+Section: Science/Biology
+
+Format: text
+Files: /usr/share/doc/last-align/last-manual.txt.gz
Added: trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-scripts
===================================================================
--- trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-scripts (rev 0)
+++ trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-scripts 2008-09-11 06:56:57 UTC (rev 2479)
@@ -0,0 +1,9 @@
+Document: last-align-scripts
+Title: LAST manual: helper scripts
+Author: Martin C. Frith and Paul B. Horton
+Abstract: This manual describes how to use the helper scripts
+ that are disributed with LAST.
+Section: Science/Biology
+
+Format: text
+Files: /usr/share/doc/last-align/last-scripts.txt
Added: trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-seeds
===================================================================
--- trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-seeds (rev 0)
+++ trunk/packages/last-align/trunk/debian/last-align.doc-base.last-align-seeds 2008-09-11 06:56:57 UTC (rev 2479)
@@ -0,0 +1,9 @@
+Document: last-align-seeds
+Title: LAST manual: chosing a seed.
+Author: Martin C. Frith and Paul B. Horton
+Abstract: This document suggests a strategy for mapping short sequence tags to
+ genomes with LAST.
+Section: Science/Biology
+
+Format: text
+Files: /usr/share/doc/last-align/tag-seeds.txt
Added: trunk/packages/last-align/trunk/debian/rules
===================================================================
--- trunk/packages/last-align/trunk/debian/rules (rev 0)
+++ trunk/packages/last-align/trunk/debian/rules 2008-09-11 06:56:57 UTC (rev 2479)
@@ -0,0 +1,16 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+
+DEB_MAKE_BUILD_TARGET = --directory src
+
+clean::
+ $(RM) src/lastdb src/lastal
+
+# The unzip command from the unzip package is needed for this one.
+# Please update debian/changelog before calling this target.
+get-orig-source:
+ [ -f ../last-$(DEB_UPSTREAM_VERSION).zip ] || uscan --force-download
+ unzip ../last-$(DEB_UPSTREAM_VERSION).zip -d..
+ tar --create --gzip --file ../last-align_$(DEB_UPSTREAM_VERSION).orig.tar.gz ../last-$(DEB_UPSTREAM_VERSION)
Property changes on: trunk/packages/last-align/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/last-align/trunk/debian/watch
===================================================================
--- trunk/packages/last-align/trunk/debian/watch (rev 0)
+++ trunk/packages/last-align/trunk/debian/watch 2008-09-11 06:56:57 UTC (rev 2479)
@@ -0,0 +1,2 @@
+version=3
+http://last.cbrc.jp/archive/last-(.*).zip
Modified: trunk/packages/last-align/trunk/src/Alignment.cc
===================================================================
--- trunk/packages/last-align/trunk/src/Alignment.cc 2008-09-11 06:56:34 UTC (rev 2478)
+++ trunk/packages/last-align/trunk/src/Alignment.cc 2008-09-11 06:56:57 UTC (rev 2479)
@@ -6,6 +6,7 @@
#include "Alphabet.hh"
#include "GeneralizedAffineGapCosts.hh"
#include "stringify.hh"
+#include <algorithm>
#include <iomanip>
#include <cassert>
Modified: trunk/packages/last-align/trunk/src/AlignmentPot.hh
===================================================================
--- trunk/packages/last-align/trunk/src/AlignmentPot.hh 2008-09-11 06:56:34 UTC (rev 2478)
+++ trunk/packages/last-align/trunk/src/AlignmentPot.hh 2008-09-11 06:56:57 UTC (rev 2479)
@@ -6,6 +6,7 @@
#ifndef ALIGNMENTPOT_HH
#define ALIGNMENTPOT_HH
#include "Alignment.hh"
+#include <algorithm>
#include <vector>
namespace cbrc{
Modified: trunk/packages/last-align/trunk/src/Alphabet.cc
===================================================================
--- trunk/packages/last-align/trunk/src/Alphabet.cc 2008-09-11 06:56:34 UTC (rev 2478)
+++ trunk/packages/last-align/trunk/src/Alphabet.cc 2008-09-11 06:56:57 UTC (rev 2479)
@@ -1,6 +1,7 @@
// Copyright 2008 Martin C. Frith
#include "Alphabet.hh"
+#include <algorithm>
#include <istream>
#include <ostream>
#include <stdexcept>
Modified: trunk/packages/last-align/trunk/src/MultiSequence.cc
===================================================================
--- trunk/packages/last-align/trunk/src/MultiSequence.cc 2008-09-11 06:56:34 UTC (rev 2478)
+++ trunk/packages/last-align/trunk/src/MultiSequence.cc 2008-09-11 06:56:57 UTC (rev 2479)
@@ -2,6 +2,7 @@
#include "MultiSequence.hh"
#include "io.hh"
+#include <algorithm>
#include <sstream>
#include <cassert>
Modified: trunk/packages/last-align/trunk/src/PeriodicSpacedSeed.cc
===================================================================
--- trunk/packages/last-align/trunk/src/PeriodicSpacedSeed.cc 2008-09-11 06:56:34 UTC (rev 2478)
+++ trunk/packages/last-align/trunk/src/PeriodicSpacedSeed.cc 2008-09-11 06:56:57 UTC (rev 2479)
@@ -1,6 +1,7 @@
// Copyright 2008 Martin C. Frith
#include "PeriodicSpacedSeed.hh"
+#include <algorithm>
#include <stdexcept>
#include <istream>
#include <ostream>
Modified: trunk/packages/last-align/trunk/src/ScoreMatrix.cc
===================================================================
--- trunk/packages/last-align/trunk/src/ScoreMatrix.cc 2008-09-11 06:56:34 UTC (rev 2478)
+++ trunk/packages/last-align/trunk/src/ScoreMatrix.cc 2008-09-11 06:56:57 UTC (rev 2479)
@@ -1,6 +1,7 @@
// Copyright 2008 Martin C. Frith
#include "ScoreMatrix.hh"
+#include <algorithm>
#include <fstream>
#include <sstream>
#include <iomanip>
Modified: trunk/packages/last-align/trunk/src/ScoreMatrix.hh
===================================================================
--- trunk/packages/last-align/trunk/src/ScoreMatrix.hh 2008-09-11 06:56:34 UTC (rev 2478)
+++ trunk/packages/last-align/trunk/src/ScoreMatrix.hh 2008-09-11 06:56:57 UTC (rev 2479)
@@ -6,6 +6,7 @@
#ifndef SCOREMATRIX_HH
#define SCOREMATRIX_HH
+#include <limits.h>
#include <string>
#include <vector>
#include <iosfwd>
Modified: trunk/packages/last-align/trunk/src/SuffixArray.hh
===================================================================
--- trunk/packages/last-align/trunk/src/SuffixArray.hh 2008-09-11 06:56:34 UTC (rev 2478)
+++ trunk/packages/last-align/trunk/src/SuffixArray.hh 2008-09-11 06:56:57 UTC (rev 2479)
@@ -18,6 +18,7 @@
#ifndef SUFFIXARRAY_HH
#define SUFFIXARRAY_HH
+#include <string>
#include <vector>
namespace cbrc{
Modified: trunk/packages/last-align/trunk/src/XdropAligner.hh
===================================================================
--- trunk/packages/last-align/trunk/src/XdropAligner.hh 2008-09-11 06:56:34 UTC (rev 2478)
+++ trunk/packages/last-align/trunk/src/XdropAligner.hh 2008-09-11 06:56:57 UTC (rev 2479)
@@ -4,6 +4,7 @@
#ifndef XDROPALIGNER_HH
#define XDROPALIGNER_HH
+#include <limits.h>
#include <vector>
namespace cbrc{
Modified: trunk/packages/last-align/trunk/src/lastal.cc
===================================================================
--- trunk/packages/last-align/trunk/src/lastal.cc 2008-09-11 06:56:34 UTC (rev 2478)
+++ trunk/packages/last-align/trunk/src/lastal.cc 2008-09-11 06:56:57 UTC (rev 2479)
@@ -17,6 +17,7 @@
#include "GeneralizedAffineGapCosts.hh"
#include "io.hh"
#include "stringify.hh"
+#include <ctime>
#include <iostream>
#include <fstream>
#include <stdexcept>
Modified: trunk/packages/last-align/trunk/src/lastdb.cc
===================================================================
--- trunk/packages/last-align/trunk/src/lastdb.cc 2008-09-11 06:56:34 UTC (rev 2478)
+++ trunk/packages/last-align/trunk/src/lastdb.cc 2008-09-11 06:56:57 UTC (rev 2479)
@@ -10,6 +10,7 @@
#include "PeriodicSpacedSeed.hh"
#include "io.hh"
#include "stringify.hh"
+#include <cstdlib>
#include <stdexcept>
#include <fstream>
#include <iostream>
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