[med-svn] [Git][med-team/lagan][master] Preparing for upload to experimental.
Steffen Möller
gitlab at salsa.debian.org
Fri Sep 7 18:46:09 BST 2018
Steffen Möller pushed to branch master at Debian Med / lagan
Commits:
690c74bd by Steffen Moeller at 2018-09-07T13:17:36Z
Preparing for upload to experimental.
- - - - -
13 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/examples
- debian/install → debian/lagan.install
- + debian/lagan.lintian-overrides
- + debian/manpages
- + debian/mlagan.1
- + debian/patches/addTest.patch
- + debian/patches/adjustPerlPaths.patch
- + debian/patches/ambiuousEnd.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,6 +1,19 @@
+lagan (2.0-2) experimental; urgency=low
+
+ * Initial release to experimental to invite peer review (Closes: #908215).
+ * Added man page for mlagan, also added *.pl scripts to /usr/bin
+ * Added embarrassingly simple test routine to run "mlagan -h"
+ * Solved compile time "ambiguity" error
+ * d/control:
+ - Bumped policy to 4.2.1
+ - Adjusted URLs to repository
+ * d/changelog: updated GSF address
+ * lintian overrides for .pl endings
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 07 Sep 2018 14:10:07 +0200
+
lagan (2.0-1) UNRELEASED; urgency=low
- * Initial release
* TODO:
- fix installation location possibly wrapper script featuring
some $lagandir path variable (/usr/lib/lagan ???)
=====================================
debian/control
=====================================
@@ -1,20 +1,20 @@
Source: lagan
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>, Steffen Moeller <moeller at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10),
libboost-dev
-Standards-Version: 4.1.1
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/lagan.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/lagan.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/lagan
+Vcs-Git: https://salsa.debian.org/med-team/lagan.git
Homepage: http://lagan.stanford.edu/lagan_web/index.shtml
Package: lagan
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
-Description: highly parametrizable pairwise global alignment program
+Description: highly parametrizable pairwise global genome sequence aligner
Lagan takes local alignments generated by CHAOS as anchors, and limits
the search area of the Needleman-Wunsch algorithm around these anchors.
.
=====================================
debian/copyright
=====================================
@@ -7,26 +7,25 @@ Files-Excluded:
Files: *
Copyright: © 2003-2006 Michael Brudno, Chuong Do, et. al.
-License: GPLv2+
+License: GPL-2.0+
Files: debian/*
Copyright: © 2012-2013 Andreas Tille <tille at debian.org>
-License: GPLv2+
+License: GPL-2.0+
-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.
+License: GPL-2.0+
+ This package 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.
+ This package 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
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>
.
- On Debian systems you can find the full text of the GPL 2+ license
- at /usr/share/common-licenses/GPL-2.
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
=====================================
debian/examples
=====================================
@@ -0,0 +1,3 @@
+sample.fasta
+sample.params
+test.score
=====================================
debian/install → debian/lagan.install
=====================================
@@ -2,5 +2,10 @@ anchors usr/bin
chaos usr/bin
glocal usr/bin
mlagan usr/bin
+prolagan usr/bin
order usr/bin
+*.pl usr/bin
utils usr/lib/lagan
+blosum62s.txt usr/lib/lagan
+blosum62.txt usr/lib/lagan
+nucmatrix.txt usr/lib/lagan
=====================================
debian/lagan.lintian-overrides
=====================================
@@ -0,0 +1,21 @@
+# Not messing with whatever defaults the community has already
+# established for maximal compatibility with existing scripts.
+lagan: script-with-language-extension usr/bin/anal_gloc.pl
+lagan: script-with-language-extension usr/bin/lagan.pl
+lagan: script-with-language-extension usr/bin/rechaos.pl
+lagan: script-with-language-extension usr/bin/slagan-mfa.pl
+lagan: script-with-language-extension usr/bin/slagan.pl
+lagan: script-with-language-extension usr/bin/supermap.pl
+lagan: script-with-language-extension usr/bin/xmfa2mfa.pl
+lagan: binary-without-manpage usr/bin/anal_gloc.pl
+lagan: binary-without-manpage usr/bin/anchors
+lagan: binary-without-manpage usr/bin/chaos
+lagan: binary-without-manpage usr/bin/glocal
+lagan: binary-without-manpage usr/bin/lagan.pl
+lagan: binary-without-manpage usr/bin/order
+lagan: binary-without-manpage usr/bin/prolagan
+lagan: binary-without-manpage usr/bin/rechaos.pl
+lagan: binary-without-manpage usr/bin/slagan-mfa.pl
+lagan: binary-without-manpage usr/bin/slagan.pl
+lagan: binary-without-manpage usr/bin/supermap.pl
+lagan: binary-without-manpage usr/bin/xmfa2mfa.pl
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/mlagan.1
=====================================
debian/mlagan.1
=====================================
@@ -0,0 +1,57 @@
+.TH MLAGAN "1" "September 2018" "mlagan" "User Commands"
+.SH NAME
+mlagan \- highly parametrizable pairwise global aligner
+.SH SYNOPSIS
+mlagan seqfile_1 seqfile_2 [... seqfile_63] [-parameters]
+.SH DESCRIPTION
+Lagan takes local alignments generated by CHAOS as anchors, and limits
+the search area of the Needleman-Wunsch algorithm around these anchors.
+.PP
+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.
+.SH OPTIONS
+.TP
+\fB\-nested\fR : runs improvement in a nested fashion
+.TP
+\fB\-postir\fR : incorporates the final improvement phase
+.TP
+\fB\-lazy\fR : uses lazy mode
+.TP
+\fB\-translate\fR : use translated anchors
+.TP
+\fB\-fastreject\fR : use fast rejection (tuned for human/mouse or closer)
+.TP
+\fB\-verbose\fR : give debug output
+.TP
+\fB\-tree\fR "(...)" : runs with given phylogenetic tree
+.TP
+\fB\-out\fR "filename": outputs to filename
+.TP
+\fB\-nucmatrixfile\fR "filename": uses given substitution matrix instead of \fI\,$LAGAN_DIR/nucmatrix.txt\/\fP
+.TP
+\fB\-version\fR : prints version info
+.PP
+\fB\-nested\fR : runs improvement in a nested fashion
+.TP
+\fB\-postir\fR : incorporates the final improvement phase
+.TP
+\fB\-lazy\fR : uses lazy mode
+.TP
+\fB\-translate\fR : use translated anchors
+.TP
+\fB\-fastreject\fR : use fast rejection (tuned for human/mouse or closer)
+.TP
+\fB\-verbose\fR : give debug output
+.TP
+\fB\-tree\fR "(...)" : runs with given phylogenetic tree
+.TP
+\fB\-out\fR "filename": outputs to filename
+.TP
+\fB\-nucmatrixfile\fR "filename": uses given substitution matrix instead of \fI\,$LAGAN_DIR/nucmatrix.txt\/\fP
+.TP
+\fB\-version\fR : prints version info
+.SH ENVIRONMENT
+The LAGAN_DIR variable specifies the location of the nucmatrix file. It
+defaults to /usr/lib/lagan, where Debian also place that file.
=====================================
debian/patches/addTest.patch
=====================================
@@ -0,0 +1,15 @@
+Index: lagan/Makefile
+===================================================================
+--- lagan.orig/Makefile
++++ lagan/Makefile
+@@ -1,5 +1,8 @@
+ all:
+- (cd src; $(MAKE))
++ $(MAKE) -C src
+ clean:
+ rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay
+- (cd src; $(MAKE) clean)
++ $(MAKE) -C src clean
++
++test: all
++ (LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]"
=====================================
debian/patches/adjustPerlPaths.patch
=====================================
@@ -0,0 +1,150 @@
+Index: lagan/anal_gloc.pl
+===================================================================
+--- lagan.orig/anal_gloc.pl
++++ lagan/anal_gloc.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ $savname1 = "";
+ $savname2 = "";
+Index: lagan/lagan.pl
+===================================================================
+--- lagan.orig/lagan.pl
++++ lagan/lagan.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ $lagandir = $ENV{LAGAN_DIR};
+ $consrate = 45;
+Index: lagan/rechaos.pl
+===================================================================
+--- lagan.orig/rechaos.pl
++++ lagan/rechaos.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ $lagandir = $ENV{LAGAN_DIR};
+
+Index: lagan/utils/cmerge2.pl
+===================================================================
+--- lagan.orig/utils/cmerge2.pl
++++ lagan/utils/cmerge2.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ use File::Basename;
+
+ $lagandir = $ENV{LAGAN_DIR};
+Index: lagan/utils/draft.pl
+===================================================================
+--- lagan.orig/utils/draft.pl
++++ lagan/utils/draft.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+ use File::Basename;
+
+ $lazyflag = 0;
+Index: lagan/utils/mextract.pl
+===================================================================
+--- lagan.orig/utils/mextract.pl
++++ lagan/utils/mextract.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ if (@ARGV < 1) {
+ print ("usage:\n mextract.pl filename [-masked]\n");
+Index: lagan/utils/mf2bin.pl
+===================================================================
+--- lagan.orig/utils/mf2bin.pl
++++ lagan/utils/mf2bin.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ # defaults
+ # constants
+Index: lagan/utils/mpretty.pl
+===================================================================
+--- lagan.orig/utils/mpretty.pl
++++ lagan/utils/mpretty.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ # defaults
+
+Index: lagan/utils/mproject.pl
+===================================================================
+--- lagan.orig/utils/mproject.pl
++++ lagan/utils/mproject.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ if (@ARGV < 2) {
+ print ("usage:\n mproject.pl filename seqname1 [seqname2 ... ]\n");
+Index: lagan/utils/mrun.pl
+===================================================================
+--- lagan.orig/utils/mrun.pl
++++ lagan/utils/mrun.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ # This script requires the environment variables:
+ # LAGAN_DIR and VISTA_DIR
+Index: lagan/utils/mrunfile.pl
+===================================================================
+--- lagan.orig/utils/mrunfile.pl
++++ lagan/utils/mrunfile.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ # This script requires the environment variables:
+ # LAGAN_DIR and VISTA_DIR
+Index: lagan/utils/mrunpairs.pl
+===================================================================
+--- lagan.orig/utils/mrunpairs.pl
++++ lagan/utils/mrunpairs.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ # This script requires the environment variables:
+ # LAGAN_DIR and VISTA_DIR
+Index: lagan/utils/msplit.pl
+===================================================================
+--- lagan.orig/utils/msplit.pl
++++ lagan/utils/msplit.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+ if (@ARGV < 1) {
+ print ("usage:\n msplit.pl filename [-masked]\n");
+Index: lagan/utils/mviz.pl
+===================================================================
+--- lagan.orig/utils/mviz.pl
++++ lagan/utils/mviz.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env perl
++#!/usr/bin/perl
+
+
+ # This script requires the environment variables:
+Index: lagan/utils/Utils.pm
+===================================================================
+--- lagan.orig/utils/Utils.pm
++++ lagan/utils/Utils.pm
+@@ -1,5 +1,3 @@
+-#!/usr/bin/env perl
+-
+ package Utils;
+ require 5.000;
+
=====================================
debian/patches/ambiuousEnd.patch
=====================================
@@ -0,0 +1,45 @@
+Index: lagan/src/glocal/rightinfluence.cpp
+===================================================================
+--- lagan.orig/src/glocal/rightinfluence.cpp
++++ lagan/src/glocal/rightinfluence.cpp
+@@ -1,6 +1,6 @@
+ #include <rightinfluence.h>
+
+-Fragment origin, end;
++static Fragment originFrag, endFrag;
+
+ // Sets the first default owner of the whole region
+ void initRI(RI *RightInfluence, long long int scoreIndex) {
+@@ -13,22 +13,22 @@ void initRI(RI *RightInfluence, long lon
+ }
+
+ // will lose to anyone
+- origin.seq1End = 0; origin.seq2End = 0;
+- origin.seq1Start = 0; origin.seq2Start = 0;
++ originFrag.seq1End = 0; originFrag.seq2End = 0;
++ originFrag.seq1Start = 0; originFrag.seq2Start = 0;
+
+ // hack to aid winner selection
+- origin.score = -1;
+- end.score = -2;
+- origin.totalScore = end.totalScore = 0;
++ originFrag.score = -1;
++ endFrag.score = -2;
++ originFrag.totalScore = endFrag.totalScore = 0;
+
+ // will win against anyone
+- end.seq1End = 0; end.seq2End = 0;
+- end.seq1Start = 0; end.seq2Start = 0;
++ endFrag.seq1End = 0; endFrag.seq2End = 0;
++ endFrag.seq1Start = 0; endFrag.seq2Start = 0;
+
+- origin.back = NULL;
++ originFrag.back = NULL;
+
+- RightInfluence->act[-INF] = &origin;
+- RightInfluence->act[+INF] = &end;
++ RightInfluence->act[-INF] = &originFrag;
++ RightInfluence->act[+INF] = &endFrag;
+ }
+
+
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,5 @@
do_not_define_conflicting_getline.patch
gcc-4.8.patch
+ambiuousEnd.patch
+addTest.patch
+adjustPerlPaths.patch
=====================================
debian/rules
=====================================
@@ -8,3 +8,7 @@
get-orig-source:
mkdir -p ../tarballs
uscan --verbose --force-download --repack-compression xz --destdir=../tarballs
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -f prolagan
View it on GitLab: https://salsa.debian.org/med-team/lagan/commit/690c74bd2f44de1a70375de1107789db15357798
--
View it on GitLab: https://salsa.debian.org/med-team/lagan/commit/690c74bd2f44de1a70375de1107789db15357798
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