From 4f8fc5052a0ecc0e116c50eea050fff73fa51cd5 Mon Sep 17 00:00:00 2001 From: wen Date: Thu, 13 Dec 2012 13:27:13 +0000 Subject: Update to 2.1, from Wen Heping(myself) in PR 43395 Add LICENSE Remove unneeded MESSAGE file Upstream changes: Version 2.1 ---------------------------------------------------------------------- * Fixed bug 196 "clustalx: user feedback about use of secondary structure printed to console" - secondary structure is now used if specified in Alignment -> Alignment Parameters -> Secondary Structure Parameters UserParameters->getGui() should be used when ClustalW code needs to know if a function has been called from ClustalX * Fixed bug 204 "Nexus alignment format contain invalid line" - the amino acid alphabet line has been removed * Missing/corrupted file names in ClustalX status messages have been fixed * Fixed bug 175 "msf/pileup files cannot be read if sequences names are all numbers" - this happened if a line such as 528244 .......... .......... .......... .......... .......... was present in the first block of the file * Fixed bug 192 "Alignment in Phylip Format broken for big Alignments" * Fixed bug 198 "Warning about divergent sequences gets printed to console in ClustalX" * Fixed bug 151 "clustalx doesn't switch to profile alignment mode when profile12 is given on cmdline" ---------------------------------------------------------------------- Version 2.0.12 ---------------------------------------------------------------------- * Fixed bug 189 "Fixed filename used for iteration": Now Creating temporary file and added error check * Fixed bug 180 "Pairwise NJ tree: final bracket missing" * Fixed bug 178 "Seg-fault on 64bit when -quicktree -upgma for sequences with high identity": Using relative error now to avoid unsafe comparison which led to incorrect branching * Fixed Bug 176 "iteration doesn't iterate if -usetree is used as well" * Fixed bug 162 "percent identity file option in clustalW not working": Added -pim as command line option. See help * Fixed bug 155 "upgma trees cannot be read" * Fixed bug 147 "report duplicate sequences": "ClustalW/X now report offending sequences which are empty, duplicates etc * Fixed bug 134 "Exit when encountering unrecognized cmdline params": ClustalW now exits when encountering invalid values for command line arguments instead of just reverting to default values * Fixed bug 185 "clustal alignments differ between interactive and commandline mode" window-gap and ktuple initialisation now fixed and made the same between commandline and interactive mode * Fixed bug 184 "error messages are send to stdout" * Fixed bug when weights are 0, and nseq > INT_SCALE_FACTOR in UPGMA code (see RootedGuideTree.cpp) * General code cleanup - Introduced return values where control reached end of non-void function - Removed unused variables - Removed comparison between signed and unsigned integer expressions - Removed deprecated conversion from string constant to char* ---------------------------------------------------------------------- Version 2.0.11 ---------------------------------------------------------------------- * fixed file extension bug 166 in interactive mode * Fixed bug 169, memory violation for DNA/RNA k-tuple * Cut down distance calculation, symmetric matrix ---------------------------------------------------------------------- Version 2.0.10 ---------------------------------------------------------------------- * Fixed g++-4.3 compilation errors * Added new -quiet command line flag * Added new -stats= command line flag * Fixed bug 142: command separator can now be mixed "/" and "-" on all platforms * Fixed bug 141: profile merging and saving failed * Fixed bug 139: saving of column quality scores * Updated help files (new flags, new colour parameter format) ---------------------------------------------------------------------- Version 2.0.9 ---------------------------------------------------------------------- * GUI now responding and giving feedback during alignment * automatic automake os detection * new OS_ define (set by clustalw/configure clustalx/clustalx.pro) * got rid of qt3 dependencies * removed QScrollArea bug workaround (fixed in Qt 4.3) * Fixed bug 135: Last sequence and last residue not displayed on MacOSX * Fixed bug 123: secondary structure profile alignment in clustalX on Mac * Fixed g++-4.3 build error (include climits.h) ---------------------------------------------------------------------- Version 2.0.8 ---------------------------------------------------------------------- * Implemented maxseqlen cmdline switch * Updated help-file * Fixed Bug 123: loading profile using gap penalties (ClustalX, Mac) * Fixed bug 133: providing profiles on command line fails (ClustalX) * Fixed bug 125: Angle bracket inside sequence * Fixed bug 129: Early exit on empty sequence * Fixed a couple of possible memory leaks ---------------------------------------------------------------------- Version 2.0.7 ---------------------------------------------------------------------- * Fixed bug 121: CRLF in sequence names (Pearson) are not trimmed * Fixed bug 122: convert option broken * Fixed reopened bug 114: profile alignment input didn't work with new getSeqRange routines * Fixed bug 119: build with g++ 4.3 ---------------------------------------------------------------------- Version 2.0.6 ---------------------------------------------------------------------- * Fixed bug 77: fasta input performance issue * Fixed bug 114: segfault while doing profile alignment with secondary structure mask * Removed unncessary id console output in EMBLFileParser.cpp * Fixed Bugs 108 and 109 and allowed mixed-case command line options ---------------------------------------------------------------------- Version 2.0.5 ---------------------------------------------------------------------- * Fixed bug 105: Disallowed combination of "Reset Gaps" and Iteration in GUI * Fixed bug 104 "reset all gaps doesn't work" * Changed command line separator for Mac to hyphen instead slash * Fixed full command line parsing for ClustalX after help flag ---------------------------------------------------------------------- Version 2.0.4 ---------------------------------------------------------------------- * Updated URLs in help files * Fixed bug 96: error message when loading alignment with identical sequence names * Made console output look more like 1.83 * Fixed bug 100: "Scores in clustalw2.0 don't match clustalw1.83" getMatrix was called with wrong scaling factor * Fixed bug 99: "stars in input not ignored" Asterisks were changed to gaps in alignment * New command line option: -fullhelp which dumps the built-in help file content. * Quickfix for bug 94 "quicktree seqfault" ---------------------------------------------------------------------- <= Version 2.0.3 ---------------------------------------------------------------------- * Added LICENSE file to distribution This file contains the information about commercial licensing of clustal as well as FAQ for licensing issues * Added README file to distribution This is the file that lists the files and directories on the Clustal FTP site. It also includes acknowledgements of people who have contributed binaries * Removed .pro Qt file from the distribution pro-file should be generated anew using qmake and modified according to build requirements, i.e. no need for version control. * Fixed bug where ClustalX2 was not processing command line args * Fixed Segfault on opening helpfile. Happened on Linux only with -O2 and when calling binary directly, not using the wrapper * Added debian packaging files * Added support for help command line flag GUI/xmenus version When requesting help file, graphical version of command line help is displayed (1.83 tried to open clustalw help) * Added complete automake (configure etc) system according to the following websites: - http://www.openismus.com/documents/linux/automake/automake.shtml - http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html * clustalw files source files have been moved to subdir * Fixed bug #53 change MAXNAMESTODISPLAY back to 10 from 30. This fixes problem of large amount of space between sequence name and actual alignment in clustal output files * This solves bug #72 with long lines (5000+) in fasta files changed code to use strings rather than arrays. Needed to add delim parameter to getline in order to read files formatted for different OSs on different platforms. * Fixed Bug 79: "The count of amino acids in the ClustalX Postscript output not correct" Off-by-one issue * ClustalX and ClustalW version numbers are now the same and defined in ClustalW code (automake) * Fixed problem with compilation of ClustalX2 with gcc3 avoiding gcc3 error message: cannot declare member function QDir::currentPath' * Target now clustalw2 instead of clustalw * Fixed Bug 46 added in aminoacid code O for pyrrolysine * Fixed bug 89 changed clustalw2.0 to conform to 1.83 behaviour for width of sequence ID and alignment * Fixed bug 90 changed clustalw2.0 to conform to 1.83 behaviour leading spaces are stripped from FASTA identifiers. * Fixed bug 91 Clustalw2.0 now handles pseudo-FASTA/MoST format files. Strips out numbers and spaces. --- biology/clustalw/MESSAGE | 18 ------------------ biology/clustalw/Makefile | 30 +++++++----------------------- biology/clustalw/PLIST | 8 ++------ biology/clustalw/distinfo | 11 ++++------- biology/clustalw/patches/patch-aa | 13 ------------- biology/clustalw/patches/patch-ab | 14 -------------- biology/clustalw/patches/patch-interface.c | 13 ------------- 7 files changed, 13 insertions(+), 94 deletions(-) delete mode 100644 biology/clustalw/MESSAGE delete mode 100644 biology/clustalw/patches/patch-aa delete mode 100644 biology/clustalw/patches/patch-ab delete mode 100644 biology/clustalw/patches/patch-interface.c (limited to 'biology') diff --git a/biology/clustalw/MESSAGE b/biology/clustalw/MESSAGE deleted file mode 100644 index 77eb1381117..00000000000 --- a/biology/clustalw/MESSAGE +++ /dev/null @@ -1,18 +0,0 @@ -=========================================================================== -$NetBSD: MESSAGE,v 1.3 2004/08/16 23:34:58 ben Exp $ - -POLICY ON COMMERCIAL DISTRIBUTION OF CLUSTAL W - -Clustal W is freely available to the user community. However, Clustal -W is increasingly being distributed as part of commercial sequence -analysis packages. To help us safeguard future maintenance and -development, commercial distributors of Clustal W must take out a -NON-EXCLUSIVE LICENCE. Anyone wishing to commercially distribute -version 1.83 of Clustal W should contact the authors unless they have -previously taken out a licence. - - gibson@embl-heidelberg.de - thompson@embl-heidelberg.de - d.higgins@ucc.ie - -=========================================================================== diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile index 4899a7c60ab..df0c9789f33 100644 --- a/biology/clustalw/Makefile +++ b/biology/clustalw/Makefile @@ -1,36 +1,20 @@ -# $NetBSD: Makefile,v 1.12 2012/09/11 20:32:11 asau Exp $ +# $NetBSD: Makefile,v 1.13 2012/12/13 13:27:13 wen Exp $ -DISTNAME= clustalw1.83.UNIX -PKGNAME= clustalw-1.83 +DISTNAME= clustalw-2.1 CATEGORIES= biology -MASTER_SITES= ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ \ - ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/ +MASTER_SITES= ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.1/ \ + http://www.clustal.org/download/current/ MAINTAINER= babafou@babafou.eu.org HOMEPAGE= http://bips.u-strasbg.fr/fr/Documentation/ClustalW/ COMMENT= General purpose multiple alignment program for DNA or proteins +LICENSE= gnu-gpl-v3 AND gnu-lgpl-v3 PKG_INSTALLATION_TYPES= overwrite pkgviews -MAKE_FILE= makefile -BUILD_TARGET= clustalw -WRKSRC= ${WRKDIR}/clustalw1.83 - -MAKE_FLAGS+= CC=${CC:Q} +GNU_CONFIGURE= yes +USE_LANGUAGES= c c++ INSTALLATION_DIRS= bin -post-patch: - @${SED} -e 's:@PREFIX@:${PREFIX}:' < ${WRKSRC}/clustalw.c \ - > ${WRKSRC}/clustalw.c.tmp \ - && ${MV} ${WRKSRC}/clustalw.c.tmp ${WRKSRC}/clustalw.c - -do-install: - ${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${DESTDIR}${PREFIX}/bin - ${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/clustalw - for f in clustalv.doc clustalw.doc clustalw.ms clustalw_help; do \ - ${INSTALL_DATA} ${WRKSRC}/$$f \ - ${DESTDIR}${PREFIX}/share/doc/clustalw; \ - done - .include "../../mk/bsd.pkg.mk" diff --git a/biology/clustalw/PLIST b/biology/clustalw/PLIST index 637727a70be..674a7a77ec4 100644 --- a/biology/clustalw/PLIST +++ b/biology/clustalw/PLIST @@ -1,6 +1,2 @@ -@comment $NetBSD: PLIST,v 1.2 2009/06/14 17:34:33 joerg Exp $ -bin/clustalw -share/doc/clustalw/clustalv.doc -share/doc/clustalw/clustalw.doc -share/doc/clustalw/clustalw.ms -share/doc/clustalw/clustalw_help +@comment $NetBSD: PLIST,v 1.3 2012/12/13 13:27:13 wen Exp $ +bin/clustalw2 diff --git a/biology/clustalw/distinfo b/biology/clustalw/distinfo index d1f33f6da92..23a17aaae23 100644 --- a/biology/clustalw/distinfo +++ b/biology/clustalw/distinfo @@ -1,8 +1,5 @@ -$NetBSD: distinfo,v 1.5 2012/10/20 22:02:07 joerg Exp $ +$NetBSD: distinfo,v 1.6 2012/12/13 13:27:13 wen Exp $ -SHA1 (clustalw1.83.UNIX.tar.gz) = 801ce911749171471b7964a1cff93c53c876c282 -RMD160 (clustalw1.83.UNIX.tar.gz) = 20c0ec7739be6747ae08220e5abf2bae412f039e -Size (clustalw1.83.UNIX.tar.gz) = 166863 bytes -SHA1 (patch-aa) = 96f95acb4a312c96440275ca65f7f908c9b9032f -SHA1 (patch-ab) = 75fb21b88132bdf18e7f6bc13d1d35051a1babea -SHA1 (patch-interface.c) = 4c5f76efee503d55aafec87edcb5cbb40f71579d +SHA1 (clustalw-2.1.tar.gz) = f29784f68585544baa77cbeca6392e533d4cf433 +RMD160 (clustalw-2.1.tar.gz) = e193769955a6270797fcb039ca398a4b59d9248d +Size (clustalw-2.1.tar.gz) = 350761 bytes diff --git a/biology/clustalw/patches/patch-aa b/biology/clustalw/patches/patch-aa deleted file mode 100644 index db1644e8641..00000000000 --- a/biology/clustalw/patches/patch-aa +++ /dev/null @@ -1,13 +0,0 @@ -$NetBSD: patch-aa,v 1.1.1.1 1999/07/28 20:07:01 rh Exp $ - ---- clustalw.c.orig Fri Jan 16 04:44:05 1998 -+++ clustalw.c Tue Feb 16 11:58:13 1999 -@@ -33,7 +33,7 @@ - #ifdef MSDOS - char *help_file_name = "clustalw.hlp"; - #else -- char *help_file_name = "clustalw_help"; -+ char *help_file_name = "@PREFIX@/share/doc/clustalw/clustalw_help"; - #endif - - sint max_names; /* maximum length of names in current alignment file */ diff --git a/biology/clustalw/patches/patch-ab b/biology/clustalw/patches/patch-ab deleted file mode 100644 index 30350a74a67..00000000000 --- a/biology/clustalw/patches/patch-ab +++ /dev/null @@ -1,14 +0,0 @@ -$NetBSD: patch-ab,v 1.1.1.1 1999/07/28 20:07:01 rh Exp $ - ---- amenu.c.orig Mon Dec 8 08:49:12 1997 -+++ amenu.c Sat Apr 10 22:07:58 1999 -@@ -13,7 +13,9 @@ - static jmp_buf jmpbuf; - #ifndef VMS - #ifndef AIX -+#ifndef BADSIG - #define BADSIG (void (*)())-1 -+#endif - #endif - #endif - diff --git a/biology/clustalw/patches/patch-interface.c b/biology/clustalw/patches/patch-interface.c deleted file mode 100644 index f1666bda383..00000000000 --- a/biology/clustalw/patches/patch-interface.c +++ /dev/null @@ -1,13 +0,0 @@ -$NetBSD: patch-interface.c,v 1.1 2012/10/20 22:02:07 joerg Exp $ - ---- interface.c.orig 2012-10-20 14:27:11.000000000 +0000 -+++ interface.c -@@ -210,7 +210,7 @@ static sint check_param(char **args,char - Boolean name1 = FALSE; - sint ajb; - -- if(args[0]==NULL) return; -+ if(args[0]==NULL) return -1; - - - -- cgit v1.2.3