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=<file> 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.diff -r1.3 -r0 pkgsrc/biology/clustalw/MESSAGE
(wen)
@@ -1,36 +1,20 @@ | @@ -1,36 +1,20 @@ | |||
1 | # $NetBSD: Makefile,v 1.12 2012/09/11 20:32:11 asau Exp $ | 1 | # $NetBSD: Makefile,v 1.13 2012/12/13 13:27:13 wen Exp $ | |
2 | 2 | |||
3 | DISTNAME= clustalw1.83.UNIX | 3 | DISTNAME= clustalw-2.1 | |
4 | PKGNAME= clustalw-1.83 | |||
5 | CATEGORIES= biology | 4 | CATEGORIES= biology | |
6 | MASTER_SITES= ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ \ | 5 | MASTER_SITES= ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.1/ \ | |
7 | ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/ | 6 | http://www.clustal.org/download/current/ | |
8 | 7 | |||
9 | MAINTAINER= babafou@babafou.eu.org | 8 | MAINTAINER= babafou@babafou.eu.org | |
10 | HOMEPAGE= http://bips.u-strasbg.fr/fr/Documentation/ClustalW/ | 9 | HOMEPAGE= http://bips.u-strasbg.fr/fr/Documentation/ClustalW/ | |
11 | COMMENT= General purpose multiple alignment program for DNA or proteins | 10 | COMMENT= General purpose multiple alignment program for DNA or proteins | |
11 | LICENSE= gnu-gpl-v3 AND gnu-lgpl-v3 | |||
12 | 12 | |||
13 | PKG_INSTALLATION_TYPES= overwrite pkgviews | 13 | PKG_INSTALLATION_TYPES= overwrite pkgviews | |
14 | 14 | |||
15 | MAKE_FILE= makefile | 15 | GNU_CONFIGURE= yes | |
16 | BUILD_TARGET= clustalw | 16 | USE_LANGUAGES= c c++ | |
17 | WRKSRC= ${WRKDIR}/clustalw1.83 | |||
18 | ||||
19 | MAKE_FLAGS+= CC=${CC:Q} | |||
20 | 17 | |||
21 | INSTALLATION_DIRS= bin | 18 | INSTALLATION_DIRS= bin | |
22 | 19 | |||
23 | post-patch: | |||
24 | @${SED} -e 's:@PREFIX@:${PREFIX}:' < ${WRKSRC}/clustalw.c \ | |||
25 | > ${WRKSRC}/clustalw.c.tmp \ | |||
26 | && ${MV} ${WRKSRC}/clustalw.c.tmp ${WRKSRC}/clustalw.c | |||
27 | ||||
28 | do-install: | |||
29 | ${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${DESTDIR}${PREFIX}/bin | |||
30 | ${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/clustalw | |||
31 | for f in clustalv.doc clustalw.doc clustalw.ms clustalw_help; do \ | |||
32 | ${INSTALL_DATA} ${WRKSRC}/$$f \ | |||
33 | ${DESTDIR}${PREFIX}/share/doc/clustalw; \ | |||
34 | done | |||
35 | ||||
36 | .include "../../mk/bsd.pkg.mk" | 20 | .include "../../mk/bsd.pkg.mk" |
@@ -1,6 +1,2 @@ | @@ -1,6 +1,2 @@ | |||
1 | @comment $NetBSD: PLIST,v 1.2 2009/06/14 17:34:33 joerg Exp $ | 1 | @comment $NetBSD: PLIST,v 1.3 2012/12/13 13:27:13 wen Exp $ | |
2 | bin/clustalw | 2 | bin/clustalw2 | |
3 | share/doc/clustalw/clustalv.doc | |||
4 | share/doc/clustalw/clustalw.doc | |||
5 | share/doc/clustalw/clustalw.ms | |||
6 | share/doc/clustalw/clustalw_help |
@@ -1,8 +1,5 @@ | @@ -1,8 +1,5 @@ | |||
1 | $NetBSD: distinfo,v 1.5 2012/10/20 22:02:07 joerg Exp $ | 1 | $NetBSD: distinfo,v 1.6 2012/12/13 13:27:13 wen Exp $ | |
2 | 2 | |||
3 | SHA1 (clustalw1.83.UNIX.tar.gz) = 801ce911749171471b7964a1cff93c53c876c282 | 3 | SHA1 (clustalw-2.1.tar.gz) = f29784f68585544baa77cbeca6392e533d4cf433 | |
4 | RMD160 (clustalw1.83.UNIX.tar.gz) = 20c0ec7739be6747ae08220e5abf2bae412f039e | 4 | RMD160 (clustalw-2.1.tar.gz) = e193769955a6270797fcb039ca398a4b59d9248d | |
5 | Size (clustalw1.83.UNIX.tar.gz) = 166863 bytes | 5 | Size (clustalw-2.1.tar.gz) = 350761 bytes | |
6 | SHA1 (patch-aa) = 96f95acb4a312c96440275ca65f7f908c9b9032f | |||
7 | SHA1 (patch-ab) = 75fb21b88132bdf18e7f6bc13d1d35051a1babea | |||
8 | SHA1 (patch-interface.c) = 4c5f76efee503d55aafec87edcb5cbb40f71579d |