[med-svn] r5030 - in trunk/packages/acedb/trunk/debian: . patches
Steffen Möller
moeller at alioth.debian.org
Sun Jul 11 04:33:24 UTC 2010
Author: moeller
Date: 2010-07-11 04:33:15 +0000 (Sun, 11 Jul 2010)
New Revision: 5030
Added:
trunk/packages/acedb/trunk/debian/patches/blxview_gtk_namespace_conflict.patch
trunk/packages/acedb/trunk/debian/patches/dotter_help.patch
trunk/packages/acedb/trunk/debian/patches/efetch_help.patch
Modified:
trunk/packages/acedb/trunk/debian/README.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/belvu.1
trunk/packages/acedb/trunk/debian/changelog
trunk/packages/acedb/trunk/debian/control
trunk/packages/acedb/trunk/debian/copyright
trunk/packages/acedb/trunk/debian/patches/series
trunk/packages/acedb/trunk/debian/rules
Log:
Series of updates for a reupload.
Modified: trunk/packages/acedb/trunk/debian/README.Debian
===================================================================
--- trunk/packages/acedb/trunk/debian/README.Debian 2010-07-10 20:54:01 UTC (rev 5029)
+++ trunk/packages/acedb/trunk/debian/README.Debian 2010-07-11 04:33:15 UTC (rev 5030)
@@ -2,12 +2,13 @@
----------------
To package ACEDB is a long term project that will grow with demands.
+The initial packager was only interested in a very small subset, i.e.
+the relatively small tools belvu, dotter and efetch, and has not
+the slightest understanding of the rest. If there is not a sudden
+raise of an ACEDB community eager to extend this packaging effort,
+or other packages demanding parts of it, the remaining gems shall
+remain hidden in the source tree.
-The proper packaging, i.e. to reduce the size of the binaries in favour
-of an increased acceptance of the distribution's alread shipped classical
-libraries, will need a closer collaboration with upstream and/or a higher
-personal investment.
-
Whoever feels like it please go ahead.
-- Steffen Moeller <moeller at debian.org> Mon, 17 Aug 2009 14:39:57 +0200
Modified: trunk/packages/acedb/trunk/debian/acedb-other-belvu.install
===================================================================
--- trunk/packages/acedb/trunk/debian/acedb-other-belvu.install 2010-07-10 20:54:01 UTC (rev 5029)
+++ trunk/packages/acedb/trunk/debian/acedb-other-belvu.install 2010-07-11 04:33:15 UTC (rev 5030)
@@ -1 +1 @@
-bin/belvu /usr/bin
+usr/bin/belvu
Modified: trunk/packages/acedb/trunk/debian/acedb-other-dotter.install
===================================================================
--- trunk/packages/acedb/trunk/debian/acedb-other-dotter.install 2010-07-10 20:54:01 UTC (rev 5029)
+++ trunk/packages/acedb/trunk/debian/acedb-other-dotter.install 2010-07-11 04:33:15 UTC (rev 5030)
@@ -1 +1 @@
-bin/dotter /usr/bin
+usr/bin/dotter
Modified: trunk/packages/acedb/trunk/debian/acedb-other.install
===================================================================
--- trunk/packages/acedb/trunk/debian/acedb-other.install 2010-07-10 20:54:01 UTC (rev 5029)
+++ trunk/packages/acedb/trunk/debian/acedb-other.install 2010-07-11 04:33:15 UTC (rev 5030)
@@ -1 +1 @@
-bin/efetch /usr/bin
+usr/bin/efetch
Modified: trunk/packages/acedb/trunk/debian/belvu.1
===================================================================
--- trunk/packages/acedb/trunk/debian/belvu.1 2010-07-10 20:54:01 UTC (rev 5029)
+++ trunk/packages/acedb/trunk/debian/belvu.1 2010-07-11 04:33:15 UTC (rev 5030)
@@ -1,4 +1,5 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.36.
+.\" This file was generated by help2man 1.36 and then
+.\" manually tweaked a bit.
.TH BELVU "1" "August 2009" "belvu 2.19" "User Commands"
.SH NAME
belvu \- View multiple alignments in good\-looking colours.
Modified: trunk/packages/acedb/trunk/debian/changelog
===================================================================
--- trunk/packages/acedb/trunk/debian/changelog 2010-07-10 20:54:01 UTC (rev 5029)
+++ trunk/packages/acedb/trunk/debian/changelog 2010-07-11 04:33:15 UTC (rev 5030)
@@ -1,9 +1,20 @@
+acedb (4.9.39-2) unstable; urgency=low
+
+ * Cleanups in debian/copyright reaction to previous
+ rejection (Closes: #542068)
+ * Completed man pages
+ - by adding --help as an acceptable argument
+ - with the help of help2man and some
+ - considerable manual editing
+
+ -- Steffen Moeller <moeller at debian.org> Sun, 11 Jul 2010 06:27:12 +0200
+
acedb (4.9.39-1) experimental; urgency=low
- * A first part of ACEDB is packaged (Closes: #542068)
+ * A first part of ACEDB is packaged
- the belvu alignment viewer
- the dotter pairwise alignment viewer
- the efetch tool to retrieve sequences
- * No extra effort like man pages invested
+ * No extra effort like for 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 2010-07-10 20:54:01 UTC (rev 5029)
+++ trunk/packages/acedb/trunk/debian/control 2010-07-11 04:33:15 UTC (rev 5030)
@@ -13,41 +13,33 @@
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: visualisation of sequence similarity
- For the analysis of biological sequences, a general
- principle is to corresponding regions between
- related proteins, RNA or DNA.
+ For the analysis of biological sequences, a general principle is to
+ corresponding regions between related proteins, RNA or DNA.
.
- Dotter displays graphically the similarity of
- DNA or protein sequence to itself or another
- sequence.
+ Dotter displays graphically the similarity of DNA or protein sequence
+ to itself or another sequence.
-
Package: acedb-other-belvu
Provides: belvu
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: multiple sequence alignment editor
- For the analysis of biological sequences, a general
- principle is to corresponding regions between
- related proteins, RNA or DNA. Written next to
- each other, corresponding positions above each
- other, one has prepared an alignment.
+ For the analysis of biological sequences, a general principle is to
+ corresponding regions between related proteins, RNA or DNA. Written
+ next to each other, corresponding positions above each other, one has
+ prepared an alignment.
.
- Belvu is best known for its perfect implementation
- of the Stockholm format of multiple sequence alignments,
- since upstream is maintaining that. That is for
- instance used in the Pfam and Rfam databases.
+ Belvu is best known for its perfect implementation of the Stockholm
+ format of multiple sequence alignments, since upstream is maintaining
+ that. That is for instance used in the Pfam and Rfam databases.
-
Package: acedb-other
Provides: efetch
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
Description: retrieval of DNA or protein sequences
- This package collects all those smallish applications
- that acedb collects under its 'other' target of
- its Makefile.
+ This package collects all those smallish applications that acedb collects
+ under its 'other' target of its Makefile.
.
- efetch: presumably short for 'entry fetch' collects
- sequence information from common DNA and protein
- databases.
+ efetch: presumably short for 'entry fetch' collects sequence information
+ from common DNA and protein databases.
Modified: trunk/packages/acedb/trunk/debian/copyright
===================================================================
--- trunk/packages/acedb/trunk/debian/copyright 2010-07-10 20:54:01 UTC (rev 5029)
+++ trunk/packages/acedb/trunk/debian/copyright 2010-07-11 04:33:15 UTC (rev 5030)
@@ -1,25 +1,44 @@
This package was debianized by Steffen Moeller <moeller at debian.org> on
Mon, 17 Aug 2009 14:39:57 +0200.
-It was downloaded from ftp://ftp://ftp.sanger.ac.uk/pub/acedb/SUPPORTED/
+It was downloaded from ftp://ftp.sanger.ac.uk/pub/acedb/SUPPORTED/
Files: *
Upstream Authors:
- Jean Thierry-Mieg (mieg at mrc-lmb.cam.ac.uk)
- Richard Durbin <Durbin at sanger.ac.uk>
+ Andreas Stolcke <stolcke at ICSI.Berkeley.EDU>
+ Clive Brown <cgb at sanger.ac.uk>
+ Cornel Lee <clee at genome.lbl.gov>
+ Cyrus Harmon <sly at fly2.berkeley.edu>
+ Darren Platt <daz at sanger.ac.uk>
+ Dave Matthews <matthews at greengenes.cit.cornell.edu>
+ David Koblas <koblas at netcom.com>
+ David Rowley <mgardi at watdscu.waterloo.edu>
+ Detlef Wolf <D.Wolf at dkfz-heidelberg.de>
+ Ed Griffiths (edgrif at sanger.ac.uk>
+ Erik Sonnhammer <Erik.Sonnhammer at sbc.su.se> (previous addresses found in code: esr at sanger.ac.uk, Erik.Sonnhammer at cgb.ki.se)
Fred Wobus <fw at sanger.ac.uk>
- Erik Sonnhammer <Erik.Sonnhammer at sbc.su.se>
- Simon Kelley (srk at sanger.ac.uk>
- Ed Griffiths (edgrif at sanger.ac.uk>
- Jonathan Hodgkin (cgc at mrc-lmb.cam.ac.uk>
- Lincoln Stein (Whitehead)
+ Guy Decoux <decoux at moulon.inra.fr>
Ian Longden <il at sanger.ac.uk>
- Clive Brown <cgb at sanger.ac.uk>
+ Jean Thierry-Mieg (mieg at mrc-lmb.cam.ac.uk) (also found in the code: mieg at ncbi.nlm.nih.gov, mieg at kaa.cnrs-mop.fr, mieg at kaa.crbm.cnrs-mop.fr)
+ Jo Dicks <jld at bioch.ox.ac.uk>
Jonathan Hodgkin <cgc at mrc-lmb.cam.ac.uk>
+ Lincoln Stein (Whitehead)
+ Mark Martin <mmm at cetia.fr>
+ Marcel Wijkstra <wijkstra at fwi.uva.nl>
+ Martin Senger (outdated address found in code: m.senger at dkfz-heidelberg.de)
+ Neil Laister (nl1 at mrc-lmb.cam.ac.uk)
+ Petr Kocab <p.kocab at dkfz-heidelberg.de>
+ Phil Grene <pg at genome.wustl.edu>
+ Richard Bruskiewich <rbrusk at octogene.medgen.ubc.ca> (also found in code: bruskiewich at cgiar.org)
+ Richard Durbin <Durbin at sanger.ac.uk> (previous/alternative addesses found in code: rd at mrc-lmb.cam.ac.uk, rd at sanger.ac.uk, rdurbin at demon.co.uk)
Rob Clack <rnc at sanger.ac.uk>
- Detlef Wolf <D.Wolf at dkfz-heidelberg.de>
+ Simon Kelley (srk at sanger.ac.uk>
+ Stan Letovsky <letovsky at gdb.org>
+ Stefan Wiesmann <wiesmann at sanger.ac.uk>
+ Tom Boutell <boutell at netcom.com>
+ Ulrich Sauvage <ulrich at kaa.crbm.cnrs-mop.fr>
Copyright:
@@ -49,7 +68,16 @@
Detlef Wolf (D.Wolf at dkfz-heidelberg.de)
+ (C) 1995 UBC, Canada
+ Richard Bruskiewich <rbrusk at octogene.medgen.ubc.ca>
+
+
+ With no current employments
+
+ MRC LMB, UK, Richard Durbin (now Sanger Center)
+
+
License:
All code is offered at either the GNU Lesser Public License (LGPL)
Added: trunk/packages/acedb/trunk/debian/patches/blxview_gtk_namespace_conflict.patch
===================================================================
--- trunk/packages/acedb/trunk/debian/patches/blxview_gtk_namespace_conflict.patch (rev 0)
+++ trunk/packages/acedb/trunk/debian/patches/blxview_gtk_namespace_conflict.patch 2010-07-11 04:33:15 UTC (rev 5030)
@@ -0,0 +1,22 @@
+Index: acedb-4.9.39/w9/blxview.c
+===================================================================
+--- acedb-4.9.39.orig/w9/blxview.c 2010-07-10 20:55:11.000000000 +0200
++++ acedb-4.9.39/w9/blxview.c 2010-07-10 20:57:14.000000000 +0200
+@@ -3447,7 +3447,7 @@
+ /********************************************************************************
+ ** BIG PICTURE ROUTINES ***
+ ********************************************************************************/
+-static void GSettings(GtkButton *button, gpointer args)
++static void blixemGSettings(GtkButton *button, gpointer args) // namespace conflict, there is "typedef struct _GSettings GSettings;" in /usr/include/glib-2.0/gio/giotypes.h
+ {
+ blixemSettings();
+ }
+@@ -3583,7 +3583,7 @@
+ item = makeNewToolbarButton(GTK_TOOLBAR(toolbar),
+ "Settings",
+ "Open the Preferences Window",
+- (GtkSignalFunc)GSettings) ;
++ (GtkSignalFunc)blixemGSettings) ;
+
+ item = makeNewToolbarButton(GTK_TOOLBAR(toolbar),
+ "Goto", "Go to specified co-ordinates",
Added: trunk/packages/acedb/trunk/debian/patches/dotter_help.patch
===================================================================
--- trunk/packages/acedb/trunk/debian/patches/dotter_help.patch (rev 0)
+++ trunk/packages/acedb/trunk/debian/patches/dotter_help.patch 2010-07-11 04:33:15 UTC (rev 5030)
@@ -0,0 +1,21 @@
+Index: acedb-4.9.39/w9/dotterMain.c
+===================================================================
+--- acedb-4.9.39.orig/w9/dotterMain.c 2010-07-10 23:18:41.000000000 +0200
++++ acedb-4.9.39/w9/dotterMain.c 2010-07-10 23:27:00.000000000 +0200
+@@ -230,6 +230,16 @@
+ usage = messalloc(strlen(usageText) + strlen(dotterVersion) + strlen(cc_date) + 20);
+ sprintf(usage, "%s%s, compiled %s\n", usageText, dotterVersion, cc_date);
+
++ // check if any argument is --help or -help
++ int i;
++ for(i=1; i<argc; i++) {
++ if (0 == strncmp("--help",argv[i],6) || 0 == strncmp("-help",argv[i],5)) {
++ fprintf(stderr,"%s\n",usage);
++ exit(0);
++ }
++ }
++
++
+
+ while ((optc = getopt(argc, argv, optstring)) != EOF)
+ switch (optc)
Added: trunk/packages/acedb/trunk/debian/patches/efetch_help.patch
===================================================================
--- trunk/packages/acedb/trunk/debian/patches/efetch_help.patch (rev 0)
+++ trunk/packages/acedb/trunk/debian/patches/efetch_help.patch 2010-07-11 04:33:15 UTC (rev 5030)
@@ -0,0 +1,172 @@
+Index: acedb-4.9.39/w9/efetch.c
+===================================================================
+--- acedb-4.9.39.orig/w9/efetch.c 2010-07-10 22:02:36.000000000 +0200
++++ acedb-4.9.39/w9/efetch.c 2010-07-10 22:50:51.000000000 +0200
+@@ -126,25 +126,85 @@
+ -s <#> Start at position #\n\
+ -e <#> Stop at position #\n\
+ -o More options and info...\n\
++ -h shows this usage text\n\
+ \n\
+ by Erik Sonnhammer (esr at sanger.ac.uk)\n\
+ Version 2.1, ";
+
+- if (!(usage = malloc(strlen(usageText) + 102))) {
+- fprintf(stderr, "Malloc error\n");
+- exit(1);
+- }
++ char *help;
++ static char helpText[] = "\n\
++ EFETCH - retrieve entries from sequence databases.\n\
++\n\
++ Synopsis: efetch -options [database:]<query> \n\
++\n\
++ Databases: SWissprot/SP, PIR, WOrmpep/WP, EMbl, GEnbank/GB, ProDom, ProSite\n\
++\n\
++ Options:\n\
++ -a Search with Accession number\n\
++ -f Fasta format output\n\
++ -q Sequence only output (one line)\n\
++ -s <#> Start at position #\n\
++ -e <#> Stop at position #\n\
++ -o More options and info...\n\
++\n\
++ -D <dir> Specify database directory\n\
++ -H Display index header data\n\
++ -p Display entrynames in search path\n\
++ -r Print sequence in 'raw' format\n\
++ -m Fetch from mixed mini database\n\
++ -M Mini format output\n\
++ -b Do NOT reverse the order of bytes\n\
++ (SunOS, IRIX do reverse, Alpha not)\n\
++ -d <dbfile> Specify database file (avoid this)\n\
++ -i <idxfile> Specify index file (avoid this)\n\
++ -l <divfile> Specify division lookup table (avoid this)\n\
++ -B <database> Specify database (archaic)\n\
++ -A Only return entryname for accession number\n\
++ -n <name> Give the sequence this name\n\
++ -x Don't require query to match entry's name exactly (avoid)\n\
++ -w For Wormpep: also fetch cross-referenced SwissProt entry\n\
++ -h shows this help text\n\
++\n\
++\n\
++ Environment:\n\
++ SWDIR = SwissProt directory - database and EMBL index files\n\
++ PIRDIR = PIR -- \" --\n\
++ WORMDIR = Wormpep -- \" --\n\
++ EMBLDIR = EMBL -- \" --\n\
++ GBDIR = Genbank -- \" --\n\
++ PRODOMDIR = ProDom -- \" --\n\
++ PROSITEDIR = ProSite -- \" --\n\
++ DBDIR = User's own -- \" -- (fasta format)\n\
++\n\
++ SEQDB database file (default SwissProt)\n\
++ SEQDBIDX index file\n\
++ DIVTABL division lookup table\n\
++\n\
++ Ex. setenv DBDIR /pubseq/seqlibs/embl/\n\
++\n\
++ Note that Prodom family consensus seqs can be fetched by PD:_#\n\n\
++ by Erik Sonnhammer (esr at sanger.ac.uk)\n\
++ Version 2.1, ";
+
+- strcpy(usage, usageText);
+- strncat(usage, cc_date, 100);
+- strcat(usage, "\n");
++ // check if any argument is --help or -help
++ for(i=1; i<argc; i++) {
++ if (0 == strncmp("--help",argv[i],6) || 0 == strncmp("-help",argv[i],5)) {
++ if (!(help = malloc(strlen(helpText) + 102))) {
++ fprintf(stderr, "Malloc error\n");
++ exit(1);
++ }
++ strcpy(help, helpText);
++ strncat(help, cc_date, 100);
++ strcat(help, "\n");
++ fprintf(stderr,"%s\n",helpText);
++ exit(0);
++ }
++ }
+
+ /* parse command line */
+ while ((optc = getopt(argc, argv, optstring)) != -1)
+ switch (optc) {
+
+- case 'h':
+- fprintf(stderr, "\n%s\n", usage); exit(1);
+ case 'B':
+ strcpy(dbsource, optarg); break;
+ case 'a':
+@@ -166,43 +226,16 @@
+ strcpy(dbfile, optarg); break;
+ case 'H':
+ display_head=1; break;
++ case 'h':
+ case 'o':
+- printf("\n\
+- -D <dir> Specify database directory\n\
+- -H Display index header data\n\
+- -p Display entrynames in search path\n\
+- -r Print sequence in 'raw' format\n\
+- -m Fetch from mixed mini database\n\
+- -M Mini format output\n\
+- -b Do NOT reverse the order of bytes\n\
+- (SunOS, IRIX do reverse, Alpha not)\n\
+- -d <dbfile> Specify database file (avoid this)\n\
+- -i <idxfile> Specify index file (avoid this)\n\
+- -l <divfile> Specify division lookup table (avoid this)\n\
+- -B <database> Specify database (archaic)\n\
+- -A Only return entryname for accession number\n\
+- -n <name> Give the sequence this name\n\
+- -x Don't require query to match entry's name exactly (avoid)\n\
+- -w For Wormpep: also fetch cross-referenced SwissProt entry\n\
+-\n\
+-\n\
+- Environment variables:\n\
+- SWDIR = SwissProt directory - database and EMBL index files\n\
+- PIRDIR = PIR -- \" --\n\
+- WORMDIR = Wormpep -- \" --\n\
+- EMBLDIR = EMBL -- \" --\n\
+- GBDIR = Genbank -- \" --\n\
+- PRODOMDIR = ProDom -- \" --\n\
+- PROSITEDIR = ProSite -- \" --\n\
+- DBDIR = User's own -- \" -- (fasta format)\n\
+-\n\
+- SEQDB database file (default SwissProt)\n\
+- SEQDBIDX index file\n\
+- DIVTABL division lookup table\n\
+-\n\
+- Ex. setenv DBDIR /pubseq/seqlibs/embl/\n\
+-\n\
+- Note that Prodom family consensus seqs can be fetched by PD:_#\n\n");
++ if (!(help = malloc(strlen(helpText) + 102))) {
++ fprintf(stderr, "Malloc error\n");
++ exit(1);
++ }
++ strcpy(help, helpText);
++ strncat(help, cc_date, 100);
++ strcat(help, "\n");
++ fprintf(stderr,"%s\n",helpText);
+ exit(0);
+ case 'p':
+ search = 1; break;
+@@ -229,8 +262,19 @@
+ strcpy(customName, optarg); break;
+ case 'w':
+ wormpep2swiss = 1; break;
++ case '-':
++ // omit option indicator
++ break;
+ default:
++ if (!(usage = malloc(strlen(usageText) + 102))) {
++ fprintf(stderr, "Malloc error\n");
++ exit(1);
++ }
++ strcpy(usage, usageText);
++ strncat(usage, cc_date, 102);
++ strcat(usage, "\n");
+ fprintf(stderr, "\n%s\n", usage); exit(1);
++ break;
+ }
+
+ if (argc - optind != 1)
Modified: trunk/packages/acedb/trunk/debian/patches/series
===================================================================
--- trunk/packages/acedb/trunk/debian/patches/series 2010-07-10 20:54:01 UTC (rev 5029)
+++ trunk/packages/acedb/trunk/debian/patches/series 2010-07-11 04:33:15 UTC (rev 5030)
@@ -1 +1,4 @@
+blxview_gtk_namespace_conflict.patch
belvu_help.patch
+efetch_help.patch
+dotter_help.patch
Modified: trunk/packages/acedb/trunk/debian/rules
===================================================================
--- trunk/packages/acedb/trunk/debian/rules 2010-07-10 20:54:01 UTC (rev 5029)
+++ trunk/packages/acedb/trunk/debian/rules 2010-07-11 04:33:15 UTC (rev 5030)
@@ -34,8 +34,7 @@
build-indep: build-indep-stamp
build-indep-stamp: configure-stamp
-
- # Add here commands to compile the indep part of the package.
+ # Nothing to be done for indep - for now.
#$(MAKE) doc
touch $@
@@ -49,18 +48,21 @@
install: install-indep install-arch
install-indep:
- dh_testdir
- dh_testroot
- dh_prep -i
- dh_installdirs -i
- dh_install -i
+ # Nothing to be done for indep - for now.
+ #dh_testdir
+ #dh_testroot
+ #dh_prep -i
+ #dh_installdirs -i
+ #dh_install --autodest -i
install-arch:
dh_testdir
dh_testroot
dh_prep -s
dh_installdirs -s
- dh_install -s
+ if [ ! -d debian/tmp/usr/bin ]; then mkdir -p debian/tmp/usr/bin; fi
+ cp -d `find bin/ -type f -a -executable` debian/tmp/usr/bin
+ dh_install --autodest -s
# Must not depend on anything. This is to be called by
# binary-arch/binary-indep
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