[med-svn] r15211 - in trunk/packages/lagan/trunk/debian: . patches source
Andreas Tille
tille at moszumanska.debian.org
Wed Nov 20 22:03:28 UTC 2013
Author: tille
Date: 2013-11-20 22:03:28 +0000 (Wed, 20 Nov 2013)
New Revision: 15211
Added:
trunk/packages/lagan/trunk/debian/docs
trunk/packages/lagan/trunk/debian/install
trunk/packages/lagan/trunk/debian/patches/
trunk/packages/lagan/trunk/debian/patches/do_not_define_conflicting_getline.patch
trunk/packages/lagan/trunk/debian/patches/gcc-4.8.patch
trunk/packages/lagan/trunk/debian/patches/series
trunk/packages/lagan/trunk/debian/source/
trunk/packages/lagan/trunk/debian/source/format
Modified:
trunk/packages/lagan/trunk/debian/changelog
trunk/packages/lagan/trunk/debian/control
trunk/packages/lagan/trunk/debian/copyright
trunk/packages/lagan/trunk/debian/rules
Log:
Some enhancements for lagan packaging, more work needs to be done, drop TODO list into changelog
Modified: trunk/packages/lagan/trunk/debian/changelog
===================================================================
--- trunk/packages/lagan/trunk/debian/changelog 2013-11-20 22:02:32 UTC (rev 15210)
+++ trunk/packages/lagan/trunk/debian/changelog 2013-11-20 22:03:28 UTC (rev 15211)
@@ -1,5 +1,13 @@
lagan (2.0-1) UNRELEASED; urgency=low
* Initial release
+ * TODO:
+ - fix installation location possibly wrapper script featuring
+ some $lagandir path variable (/usr/lib/lagan ???)
+ - manpages
+ - permissions
+ - hardening
+ - testing
+
- -- Andreas Tille <tille at debian.org> Sun, 27 May 2012 09:07:22 +0200
+ -- Andreas Tille <tille at debian.org> Fri, 15 Nov 2013 10:31:20 +0100
Modified: trunk/packages/lagan/trunk/debian/control
===================================================================
--- trunk/packages/lagan/trunk/debian/control 2013-11-20 22:02:32 UTC (rev 15210)
+++ trunk/packages/lagan/trunk/debian/control 2013-11-20 22:03:28 UTC (rev 15211)
@@ -1,22 +1,24 @@
Source: lagan
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.3
+Build-Depends: debhelper (>= 9),
+ libboost1.54-dev
+Standards-Version: 3.9.4
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/lagan/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/lagan/trunk/
Homepage: http://lagan.stanford.edu/lagan_web/index.shtml
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/lagan/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/lagan/trunk/
Package: lagan
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: highly parametrizable pairwise global alignment program
- Lagan takes local alignments generated by CHAOS as anchors, and limits the search area of
- the Needleman-Wunsch algorithm around these anchors.
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: highly parametrizable pairwise global alignment program
+ Lagan takes local alignments generated by CHAOS as anchors, and limits
+ the search area of the Needleman-Wunsch algorithm around these anchors.
.
- Multi-LAGAN is a generalization of the pairwise algorithm to multiple sequence alignment.
- M-LAGAN performs progressive pairwise alignments, guided by a user-specified phylogenetic
- tree. Alignments are aligned to other alignments using the sum-of-pairs metric.
+ Multi-LAGAN is a generalization of the pairwise algorithm to multiple
+ sequence alignment. M-LAGAN performs progressive pairwise alignments,
+ guided by a user-specified phylogenetic tree. Alignments are aligned to
+ other alignments using the sum-of-pairs metric.
Modified: trunk/packages/lagan/trunk/debian/copyright
===================================================================
--- trunk/packages/lagan/trunk/debian/copyright 2013-11-20 22:02:32 UTC (rev 15210)
+++ trunk/packages/lagan/trunk/debian/copyright 2013-11-20 22:03:28 UTC (rev 15211)
@@ -1,10 +1,32 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Michael Brudno <brudno at cs.toronto.edu>
Source: http://lagan.stanford.edu/lagan_web/lagan20.tar.gz
+Files-Excluded:
+ prolagan
+ src/glocal/glocal
Files: *
-Copyright: © 2003 Michael Brudno, Chuong Do, et. al.
-License: GPL-v3
+Copyright: © 2003-2006 Michael Brudno, Chuong Do, et. al.
+License: GPLv2+
Files: debian/*
-Copyright: © 2012 Andreas Tille <tille at debian.org>
-License: GPL-v3
+Copyright: © 2012-2013 Andreas Tille <tille at debian.org>
+License: GPLv2+
+
+License: GPLv2+
+ 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 2 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, write to the Free Software
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ .
+ On Debian systems you can find the full text of the GPL 2+ license
+ at /usr/share/common-licenses/GPL-2.
Added: trunk/packages/lagan/trunk/debian/docs
===================================================================
--- trunk/packages/lagan/trunk/debian/docs (rev 0)
+++ trunk/packages/lagan/trunk/debian/docs 2013-11-20 22:03:28 UTC (rev 15211)
@@ -0,0 +1 @@
+Readmes/R*
Added: trunk/packages/lagan/trunk/debian/install
===================================================================
--- trunk/packages/lagan/trunk/debian/install (rev 0)
+++ trunk/packages/lagan/trunk/debian/install 2013-11-20 22:03:28 UTC (rev 15211)
@@ -0,0 +1,6 @@
+anchors usr/bin
+chaos usr/bin
+glocal usr/bin
+mlagan usr/bin
+order usr/bin
+utils usr/lib/lagan
Added: trunk/packages/lagan/trunk/debian/patches/do_not_define_conflicting_getline.patch
===================================================================
--- trunk/packages/lagan/trunk/debian/patches/do_not_define_conflicting_getline.patch (rev 0)
+++ trunk/packages/lagan/trunk/debian/patches/do_not_define_conflicting_getline.patch 2013-11-20 22:03:28 UTC (rev 15211)
@@ -0,0 +1,24 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Fri, 15 Nov 2013 10:31:20 +0100
+Description: Prevent conflicting getline by simply renaming it
+
+--- a/src/anchors.c
++++ b/src/anchors.c
+@@ -225,7 +225,7 @@ char* rolltonum(char* str) {
+ return &str[i];
+ }
+
+-int getline(FILE* infile, hll* tt) {
++int anchors_getline(FILE* infile, hll* tt) {
+ char temp[1024];
+ char* help;
+ int z, h;
+@@ -248,7 +248,7 @@ hll* parseCHAOS(FILE* infile, int* totnu
+ *totnum = 0;
+ while(!feof(infile)) {
+ tt = (hll*) malloc(sizeof(hll));
+- while (!feof(infile) && !getline(infile, tt))
++ while (!feof(infile) && !anchors_getline(infile, tt))
+ ;
+ if (feof(infile)) break;
+ if (gapfreechunks) {
Added: trunk/packages/lagan/trunk/debian/patches/gcc-4.8.patch
===================================================================
--- trunk/packages/lagan/trunk/debian/patches/gcc-4.8.patch (rev 0)
+++ trunk/packages/lagan/trunk/debian/patches/gcc-4.8.patch 2013-11-20 22:03:28 UTC (rev 15211)
@@ -0,0 +1,25 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Fri, 15 Nov 2013 10:31:20 +0100
+Description: Fix some includes to build using gcc-4.8
+
+--- a/src/utils/Glue.cpp
++++ b/src/utils/Glue.cpp
+@@ -6,6 +6,7 @@
+ #include <fstream>
+ #include <iostream>
+ #include <algorithm>
++#include <string.h>
+
+ #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt"
+ #define MAX_LINE_LENGTH 1024
+--- a/src/glocal/score.cpp
++++ b/src/glocal/score.cpp
+@@ -2,7 +2,7 @@
+ #include<score.h>
+ #include<leftinfluence.h>
+ #include<rightinfluence.h>
+-#include<fstream.h>
++#include<fstream>
+
+ extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
+
Added: trunk/packages/lagan/trunk/debian/patches/series
===================================================================
--- trunk/packages/lagan/trunk/debian/patches/series (rev 0)
+++ trunk/packages/lagan/trunk/debian/patches/series 2013-11-20 22:03:28 UTC (rev 15211)
@@ -0,0 +1,2 @@
+do_not_define_conflicting_getline.patch
+gcc-4.8.patch
Modified: trunk/packages/lagan/trunk/debian/rules
===================================================================
--- trunk/packages/lagan/trunk/debian/rules 2013-11-20 22:02:32 UTC (rev 15210)
+++ trunk/packages/lagan/trunk/debian/rules 2013-11-20 22:03:28 UTC (rev 15211)
@@ -7,4 +7,4 @@
get-orig-source:
mkdir -p ../tarballs
- uscan --verbose --force-download --destdir=../tarballs
+ uscan --verbose --force-download --repack-compression xz --destdir=../tarballs
Added: trunk/packages/lagan/trunk/debian/source/format
===================================================================
--- trunk/packages/lagan/trunk/debian/source/format (rev 0)
+++ trunk/packages/lagan/trunk/debian/source/format 2013-11-20 22:03:28 UTC (rev 15211)
@@ -0,0 +1 @@
+3.0 (quilt)
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