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author | wen <wen> | 2012-12-13 13:27:13 +0000 |
---|---|---|
committer | wen <wen> | 2012-12-13 13:27:13 +0000 |
commit | 4f8fc5052a0ecc0e116c50eea050fff73fa51cd5 (patch) | |
tree | e91477c74dfd3f518d48db206e088d691a0b3f16 /biology/clustalw | |
parent | a7c35a153fc19b1be6d431669b1cf16e6549092a (diff) | |
download | pkgsrc-4f8fc5052a0ecc0e116c50eea050fff73fa51cd5.tar.gz |
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.
Diffstat (limited to 'biology/clustalw')
-rw-r--r-- | biology/clustalw/MESSAGE | 18 | ||||
-rw-r--r-- | biology/clustalw/Makefile | 30 | ||||
-rw-r--r-- | biology/clustalw/PLIST | 8 | ||||
-rw-r--r-- | biology/clustalw/distinfo | 11 | ||||
-rw-r--r-- | biology/clustalw/patches/patch-aa | 13 | ||||
-rw-r--r-- | biology/clustalw/patches/patch-ab | 14 | ||||
-rw-r--r-- | biology/clustalw/patches/patch-interface.c | 13 |
7 files changed, 13 insertions, 94 deletions
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; - - - |