[med-svn] r3785 - in trunk/packages/acedb/trunk/debian: . patches
Steffen Möller
smoe-guest at alioth.debian.org
Mon Aug 17 23:43:24 UTC 2009
Author: smoe-guest
Date: 2009-08-17 23:43:24 +0000 (Mon, 17 Aug 2009)
New Revision: 3785
Added:
trunk/packages/acedb/trunk/debian/README.source
trunk/packages/acedb/trunk/debian/acedb-other-belvu.manpages
trunk/packages/acedb/trunk/debian/belvu.1
trunk/packages/acedb/trunk/debian/patches/
trunk/packages/acedb/trunk/debian/patches/belvu_help.patch
trunk/packages/acedb/trunk/debian/patches/series
Modified:
trunk/packages/acedb/trunk/debian/
trunk/packages/acedb/trunk/debian/acedb-other-belvu.install
trunk/packages/acedb/trunk/debian/acedb-other-dotter.install
trunk/packages/acedb/trunk/debian/acedb-other.install
trunk/packages/acedb/trunk/debian/changelog
trunk/packages/acedb/trunk/debian/control
trunk/packages/acedb/trunk/debian/copyright
trunk/packages/acedb/trunk/debian/rules
Log:
Added man page for belvu, added -v and -h options.
Property changes on: trunk/packages/acedb/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/acedb/trunk/debian/README.source
===================================================================
--- trunk/packages/acedb/trunk/debian/README.source (rev 0)
+++ trunk/packages/acedb/trunk/debian/README.source 2009-08-17 23:43:24 UTC (rev 3785)
@@ -0,0 +1,2 @@
+
+* belvu now understands '-h' as a request for help
Modified: trunk/packages/acedb/trunk/debian/acedb-other-belvu.install
===================================================================
--- trunk/packages/acedb/trunk/debian/acedb-other-belvu.install 2009-08-17 22:31:08 UTC (rev 3784)
+++ trunk/packages/acedb/trunk/debian/acedb-other-belvu.install 2009-08-17 23:43:24 UTC (rev 3785)
@@ -1 +1 @@
-bin/belvu
+bin/belvu /usr/bin
Added: trunk/packages/acedb/trunk/debian/acedb-other-belvu.manpages
===================================================================
--- trunk/packages/acedb/trunk/debian/acedb-other-belvu.manpages (rev 0)
+++ trunk/packages/acedb/trunk/debian/acedb-other-belvu.manpages 2009-08-17 23:43:24 UTC (rev 3785)
@@ -0,0 +1 @@
+debian/belvu.1
Modified: trunk/packages/acedb/trunk/debian/acedb-other-dotter.install
===================================================================
--- trunk/packages/acedb/trunk/debian/acedb-other-dotter.install 2009-08-17 22:31:08 UTC (rev 3784)
+++ trunk/packages/acedb/trunk/debian/acedb-other-dotter.install 2009-08-17 23:43:24 UTC (rev 3785)
@@ -1 +1 @@
-bin/dotter
+bin/dotter /usr/bin
Modified: trunk/packages/acedb/trunk/debian/acedb-other.install
===================================================================
--- trunk/packages/acedb/trunk/debian/acedb-other.install 2009-08-17 22:31:08 UTC (rev 3784)
+++ trunk/packages/acedb/trunk/debian/acedb-other.install 2009-08-17 23:43:24 UTC (rev 3785)
@@ -1 +1 @@
-bin/efetch
+bin/efetch /usr/bin
Added: trunk/packages/acedb/trunk/debian/belvu.1
===================================================================
--- trunk/packages/acedb/trunk/debian/belvu.1 (rev 0)
+++ trunk/packages/acedb/trunk/debian/belvu.1 2009-08-17 23:43:24 UTC (rev 3785)
@@ -0,0 +1,110 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.36.
+.TH BELVU "1" "August 2009" "belvu 2.19" "User Commands"
+.SH NAME
+belvu \- View multiple alignments in good\-looking colours.
+.SH SYNOPSIS
+belvu [options] <multiple_alignment>|\- [X options]
+.IP
+<multiple_alignment>|\- = alignment file or pipe.
+.SH DESCRIPTION
+Belvu presents multiple sequence alignments in a colourful
+biologically interpretable manner.
+.SH OPTIONS
+\fB\-c\fR Print Conservation table.
+.HP
+\fB\-l\fR <file> Load color code file.
+.HP
+\fB\-L\fR <file> Load Markup color code file.
+.HP
+\fB\-m\fR <file> Read file with matching sequence segments.
+.HP
+\fB\-r\fR Read alignment in 'raw' format (Name sequence).
+.HP
+\fB\-R\fR Do not parse coordinates when reading alignment.
+.HP
+\fB\-o\fR <format> Write alignment or tree to stdout in this format and exit.
+.IP
+Valid formats: MSF, Mul(Stockholm), Selex,
+.IP
+FastaAlign, Fasta, tree.
+.HP
+\fB\-n\fR <cutoff> Make non\-redundant to <cutoff> %identity at startup.
+.HP
+\fB\-Q\fR <cutoff> Remove columns more gappy than <cutoff>.
+.HP
+\fB\-q\fR <cutoff> Remove sequences more gappy than <cutoff>.
+.TP
+\fB\-P\fR
+Remove partial sequences at startup.
+.TP
+\fB\-C\fR
+Don't write coordinates to saved file.
+.TP
+\fB\-z\fR <char>
+Separator char between name and coordinates in saved file.
+.TP
+\fB\-a\fR
+Show alignment annotations on screen (Stockholm format only).
+.TP
+\fB\-p\fR
+Output random model probabilites for HMMER.
+.IP
+(Based on all residues.)
+.TP
+\fB\-S\fR <order>
+Sort sequences in this order.
+.IP
+a \-> alphabetically
+o \-> by Swissprot organism, alphabetically
+s \-> by score
+n \-> by Neighbor\-joining tree
+u \-> by UPGMA tree
+S \-> by similarity to first sequence
+i \-> by identity to first sequence
+.TP
+\fB\-s\fR <file>
+Read in file of scores.
+.HP
+\fB\-T\fR <method> Start up with tree calculated by method:
+.IP
+n \-> Neighbor\-joining
+u \-> UPGMA
+N \-> Neighbor\-joining, only show tree
+U \-> UPGMA, only show tree
+c \-> Don't color tree by organism
+o \-> Don't display sequence coordinates in tree
+s \-> Use Storm & Sonnhammer distance correction
+r \-> Use uncorrected distances
+.TP
+\fB\-b\fR <#>
+Print out # bootstrapped trees and exit
+.IP
+(Negative value \-> display bootstrap trees on screen)
+.TP
+\fB\-O\fR <label>
+Read organism info after this label (default OS)
+.TP
+\fB\-t\fR <title>
+Set window title.
+.TP
+\fB\-g\fR
+Draw grid line (for debugging).
+.TP
+\fB\-u\fR
+Start up with uncoloured alignment (faster).
+.TP
+\fB\-h\fR
+Show this help.
+.TP
+\fB\-v\fR
+Show version info.
+.IP
+Some X options:
+\fB\-acefont\fR <font> Main font.
+\fB\-font\fR <font> Menu font.
+.SH "SEE ALSO"
+For documentation, see: http://www.cgb.ki.se/cgb/groups/sonnhammer/Belvu.html
+.SH AUTHOR
+Erik Sonnhammer <Erik.Sonnhammer at cgb.ki.se>
+.SH VERSION
+Version 2.16, compiled Aug 18 2009
Modified: trunk/packages/acedb/trunk/debian/changelog
===================================================================
--- trunk/packages/acedb/trunk/debian/changelog 2009-08-17 22:31:08 UTC (rev 3784)
+++ trunk/packages/acedb/trunk/debian/changelog 2009-08-17 23:43:24 UTC (rev 3785)
@@ -1,5 +1,9 @@
-acedb (4.9.39-1) unstable; urgency=low
+acedb (4.9.39-1) experimental; urgency=low
- * A first part of ACEDB is packaged - the belvu alignment editor.
+ * A first part of ACEDB is packaged (Closes: #542068)
+ - the belvu alignment viewer
+ - the dotter pairwise alignment viewer
+ - the efetch tool to retrieve sequences
+ * No extra effort like man pages invested
-- Steffen Moeller <moeller at debian.org> Mon, 17 Aug 2009 14:39:57 +0200
Modified: trunk/packages/acedb/trunk/debian/control
===================================================================
--- trunk/packages/acedb/trunk/debian/control 2009-08-17 22:31:08 UTC (rev 3784)
+++ trunk/packages/acedb/trunk/debian/control 2009-08-17 23:43:24 UTC (rev 3785)
@@ -2,7 +2,7 @@
Section: science
Priority: extra
Maintainer: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper (>= 7), libreadline5-dev, libgtk2.0-dev
+Build-Depends: debhelper (>= 7), libreadline5-dev, libgtk2.0-dev, quilt
Standards-Version: 3.8.3
Homepage: http://www.acedb.org/
Modified: trunk/packages/acedb/trunk/debian/copyright
===================================================================
--- trunk/packages/acedb/trunk/debian/copyright 2009-08-17 22:31:08 UTC (rev 3784)
+++ trunk/packages/acedb/trunk/debian/copyright 2009-08-17 23:43:24 UTC (rev 3785)
@@ -3,7 +3,7 @@
It was downloaded from ftp://ftp://ftp.sanger.ac.uk/pub/acedb/SUPPORTED/
-Upstream Author(s):
+Upstream Authors:
Jean Thierry-Mieg (mieg at mrc-lmb.cam.ac.uk)
Richard Durbin <Durbin at sanger.ac.uk>
Added: trunk/packages/acedb/trunk/debian/patches/belvu_help.patch
===================================================================
--- trunk/packages/acedb/trunk/debian/patches/belvu_help.patch (rev 0)
+++ trunk/packages/acedb/trunk/debian/patches/belvu_help.patch 2009-08-17 23:43:24 UTC (rev 3785)
@@ -0,0 +1,55 @@
+--- acedb-4.9.39.orig/w9/belvu.c
++++ acedb-4.9.39/w9/belvu.c
+@@ -4914,7 +4914,8 @@
+ output_probs = 0,
+ init_tree = 0,
+ only_tree = 0,
+- show_ann = 0;
++ show_ann = 0,
++ show_help = 0;
+ float
+ makeNRinit = 0.0,
+ init_rmEmptyColumns = 0.0,
+@@ -4926,7 +4927,7 @@
+ int optc;
+ extern int optind;
+ extern char *optarg;
+- char *optstring="ab:Ccgl:L:m:n:O:o:PpQ:q:RrS:s:T:t:uz:";
++ char *optstring="ab:Ccghl:L:m:n:O:o:PpQ:q:RrS:s:T:t:uvz:";
+
+ static char *cc_date =
+ #if defined(__DATE__)
+@@ -4988,6 +4989,8 @@
+ -t <title> Set window title.\n\
+ -g Draw grid line (for debugging).\n\
+ -u Start up with uncoloured alignment (faster).\n\
++ -h Show this help.\n\
++ -v Show version info.\n\
+ \n\
+ Some X options:\n\
+ -acefont <font> Main font.\n\
+@@ -5011,6 +5014,7 @@
+ case 'C': saveCoordsOn = 0; break;
+ case 'c': verbose = 1; break;
+ case 'g': gridOn = 1; break;
++ case 'h': show_help = 1; break;
+ case 'l':
+ colorCodesFile = messalloc(strlen(optarg+1));
+ strcpy(colorCodesFile, optarg); break;
+@@ -5089,11 +5093,15 @@
+ case 't':
+ strncpy(Title, optarg, 255); break;
+ case 'u': colorRectangles = 0; break;
++ case 'v':
++ fprintf(stderr,"%s",belvuVersion);
++ exit(1);
++ break;
+ case 'z': saveSeparator = *optarg; break;
+ default : fatal("Illegal option");
+ }
+
+- if (argc-optind < 1) {
++ if (argc-optind < 1 || show_help) {
+ fprintf(stderr, "%s\n", usage);
+ exit(1);
+ }
Added: trunk/packages/acedb/trunk/debian/patches/series
===================================================================
--- trunk/packages/acedb/trunk/debian/patches/series (rev 0)
+++ trunk/packages/acedb/trunk/debian/patches/series 2009-08-17 23:43:24 UTC (rev 3785)
@@ -0,0 +1 @@
+belvu_help.patch
Modified: trunk/packages/acedb/trunk/debian/rules
===================================================================
--- trunk/packages/acedb/trunk/debian/rules 2009-08-17 22:31:08 UTC (rev 3784)
+++ trunk/packages/acedb/trunk/debian/rules 2009-08-17 23:43:24 UTC (rev 3785)
@@ -7,10 +7,18 @@
# This has to be exported to make some magic below work.
export DH_OPTIONS
-#export ACEDB_MACHINE=LINUX_4
+DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
+DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+include /usr/share/quilt/quilt.make
+DEB_BUILD_ARCH_CPU ?= $(shell dpkg-architecture -qDEB_BUILD_ARCH_CPU)
+
+ifneq (,$(filter $(DEB_HOST_ARCH_CPU), amd64 alpha ia64 s390x ppc64 sparc64))
+export ACEDB_MACHINE=LINUX_4
+else
export ACEDB_MACHINE=LINUX_64
+endif
-configure-stamp:
+configure-stamp: patch
ln -sf bin.$(ACEDB_MACHINE) bin
touch $@
@@ -31,11 +39,12 @@
#$(MAKE) doc
touch $@
-clean:
+clean:: unpatch
dh_testdir
dh_testroot
rm -f build-arch-stamp build-indep-stamp configure-stamp
- $(MAKE) clean
+ rm -fr bin.$(ACEDB_MACHINE)
+ #$(MAKE) clean
dh_clean bin
install: install-indep install-arch
More information about the debian-med-commit
mailing list