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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 ([email protected]) - Richard Durbin <[email protected]> + Andreas Stolcke <[email protected]> + Clive Brown <[email protected]> + Cornel Lee <[email protected]> + Cyrus Harmon <[email protected]> + Darren Platt <[email protected]> + Dave Matthews <[email protected]> + David Koblas <[email protected]> + David Rowley <[email protected]> + Detlef Wolf <[email protected]> + Ed Griffiths ([email protected]> + Erik Sonnhammer <[email protected]> (previous addresses found in code: [email protected], [email protected]) Fred Wobus <[email protected]> - Erik Sonnhammer <[email protected]> - Simon Kelley ([email protected]> - Ed Griffiths ([email protected]> - Jonathan Hodgkin ([email protected]> - Lincoln Stein (Whitehead) + Guy Decoux <[email protected]> Ian Longden <[email protected]> - Clive Brown <[email protected]> + Jean Thierry-Mieg ([email protected]) (also found in the code: [email protected], [email protected], [email protected]) + Jo Dicks <[email protected]> Jonathan Hodgkin <[email protected]> + Lincoln Stein (Whitehead) + Mark Martin <[email protected]> + Marcel Wijkstra <[email protected]> + Martin Senger (outdated address found in code: [email protected]) + Neil Laister ([email protected]) + Petr Kocab <[email protected]> + Phil Grene <[email protected]> + Richard Bruskiewich <[email protected]> (also found in code: [email protected]) + Richard Durbin <[email protected]> (previous/alternative addesses found in code: [email protected], [email protected], [email protected]) Rob Clack <[email protected]> - Detlef Wolf <[email protected]> + Simon Kelley ([email protected]> + Stan Letovsky <[email protected]> + Stefan Wiesmann <[email protected]> + Tom Boutell <[email protected]> + Ulrich Sauvage <[email protected]> Copyright: @@ -49,7 +68,16 @@ Detlef Wolf ([email protected]) + (C) 1995 UBC, Canada + Richard Bruskiewich <[email protected]> + + + 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 ([email protected])\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 ([email protected])\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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
