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2012-12-13Update to 2.1, from Wen Heping(myself) in PR 43395wen7-94/+13
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.
2012-11-16Don't redefine local variables.joerg4-1/+72
2012-11-16Implicit int is not valid C++.joerg2-1/+15
2012-11-01+ plinkseqasau1-1/+2
2012-11-01Import PLINK/SEQ version 0.08 as biology/plinkseqasau4-0/+46
Packaged by Jason Bacon for pkgsrc-wip. PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.
2012-10-23Remove xextproto/buildlink3.mk in most cases where it occurs withwiz1-2/+1
libXext/buildlink3.mk, now that it is included there. Leave the places where its API version is set or variables from it are used directly (about 3 packages).
2012-10-21Add CONFLICTS between "azara" and "connect"cheusov1-2/+4
2012-10-21Fix pkglint warnings; Clean-upscheusov1-16/+8
2012-10-20Don't return without value in non-void function.joerg2-1/+15
2012-10-16Recursive bump for new gtkglext pangox-compat dependency.wiz1-2/+2
2012-10-08Revbump after updating graphics/pangoadam3-6/+6
2012-10-04Bump revision for packages with changed CONFLICTS (PYTHON_SELF_CONFLICT)cheusov1-2/+2
2012-10-03CONFLICTS between python modulescheusov1-2/+3
2012-10-03Bump all packages that use perl, or depend on a p5-* package, orwiz5-9/+10
are called p5-*. I hope that's all of them.
2012-10-02Mass recursive bump after the dependence fix of the "cairo" packagetron3-6/+6
requested by Thomas Klausner.
2012-09-16CONFLICTS with generate-[0-9]*; ++pkgrevisioncheusov1-1/+4
2012-09-15recursive bump from libffi shlib major bumpobache3-6/+6
(additionaly, reset PKGREVISION of qt4-* sub packages from base qt4 update)
2012-09-14Fix PKGNAME.asau1-1/+2
2012-09-14+ plinkasau1-1/+2
2012-09-14Remove errorneously imported backup file. (Why was it not ignored??)asau1-1/+0
2012-09-14Import PLINK 1.07 as biology/plinkasau6-0/+134
From Jason Bacon via pkgsrc-wip. PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.
2012-09-11"user-destdir" is default these daysasau31-88/+31
2012-09-07Revbump after updating graphics/cairoadam3-5/+6
2012-08-30more omf-scrollkeeper missingdrochner1-1/+2
2012-08-16Update to 0.12.13ryoon2-6/+6
Changelog: Version 0.12.13 GChemPaint: * Fix View::BuildSVG() and View::BuildEPS() which were missing the trailing 0. * Fix loading of arrows inside a group. [#27032]
2012-07-03Update to 0.12.12ryoon3-9/+9
Changelog: Version 0.12.12 GCrystal: * Fix atoms loading. * Fix infinite loop condition. [#36583] Version 0.12.11 GChemPaint: * fixed text position serialization. [#34947] * fixed crash when selecting the alignment item inside a mechanism step. [#35626]
2012-06-14Recursive PKGREVISION bump for libxml2 buildlink addition.sbd5-7/+10
2012-04-08All supported python versions in pkgsrc support eggs, so removewiz1-2/+2
${PLIST.eggfile} from PLISTs and support code from lang/python.
2012-04-08Remove python24 and all traces of it from pkgsrc.wiz1-3/+1
Remove devel/py-ctypes (only needed by and supporting python24). Remove PYTHON_VERSIONS_ACCEPTED and PYTHON_VERSIONS_INCOMPATIBLE lines that just mirror defaults now. Miscellaneous cleanup while editing all these files.
2012-03-03More pcre PKGREVISION bumps.wiz1-2/+2
2012-03-03Recursive bump for pcre-8.30* (shlib major change)wiz2-4/+4
2012-02-07Add csh scripts to REPLACE_CSH and add USE_TOOLS+=csh:runsbd1-2/+5
Bump PKGREVISION
2012-02-06Revbump forwiz3-4/+6
a) tiff update to 4.0 (shlib major change) b) glib2 update 2.30.2 (adds libffi dependency to buildlink3.mk) Enjoy.
2012-01-14Update to Gromacs 4.5.5asau3-8/+25
Notable changes in Gromacs 4.5.5: * Improved pdb2gmx -chainsep option and reintroduced the -merge option. * Fixed mdrun file appending truncating files to 0 bytes when continuation runs stopped before writing new output. * Fixed COM pulling with multiple constraints checking the convergence of one constraint instead of all. * Fixed some dihedrals in sugars in Gromos53a5/6 working on the wrong atoms. * AmberGS force field is now based on Amber94 instead of Amber96. * Moved hydrogens in Charmm27 protein termini to separate charge groups and added ACE and CT3 residue types. * Many small fixes which avoid termination with fatal errors or crashes in mdrun and tools. * Many small updates to the manual pages of programs.
2012-01-08Update to 1.6.13.ryoon2-8/+7
Changelog: Fixes and enhancements in chemtool 1.6.13 - New export option "ASY" for Asymptote files (http://asymptote.sourceforge.net) - Added support for Unicode symbol characters inserted e.g. by cut-and-paste from LibreOffice - Fixed build with newer linkers that do not resolve indirect requirements automatically - Rewritten logic for choosing to include national language support during build - Fixed crash on startup due to errors in menu icon setup - Batch mode could crash due to incomplete initialisation of color arrays - Undo/redo in "move fragment"-mode did not work as intended - Default extension is now appended to the save filename as needed - Fixed exporting to files or directories containing spaces in their names
2011-12-09PKGREV bump for libXp-less openmotifdrochner1-2/+2
2011-11-25Remove concurrently created patch.joerg2-14/+1
2011-11-24Fix build with GCC 4.5joerg2-1/+14
2011-11-23biology/mummer: Put sort function in scopemarino2-1/+14
Add <algorithm> header for sort, DragonFly's compiler needs it. No PKGREVISION bump required.
2011-11-22Update to 0.12.10ryoon2-7/+6
Changelog: Version 0.12.10 GCrystal: * show only atoms from the first crystal when loading a CIF file with several structures. * don't crash when loading a file with invalid atoms. * don't display two atoms at the same position. * don't loose the radius ratio on serialization. Other: * fix build with most recent glib-2.0 and xulrunner. * enhanced translation: de.
2011-11-01Recursive bump for graphics/freetype2 buildlink addition.sbd1-1/+2
2011-11-01Recursive bump for graphics/freetype2 buildlink addition.sbd2-2/+4
2011-10-31Initial import of primer3.brook6-1/+96
Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.
2011-10-28python24 is not acceptable.obache1-1/+3
2011-10-27Update py-mol to 1.4.1.obache3-39/+238
many improvements and bug fixes.
2011-10-07Fix impossible depends.dholland1-2/+2
2011-10-05Add bodr, chemical-mime-data, gnome-chemistry-utils, and openbabel.ryoon1-1/+5
2011-10-05Reset MAINTAINER, because no response.ryoon2-4/+4
2011-10-05Initial import of gnome-chemistry-utils-0.12.9 from wip/gnome-chemistry-utilsryoon4-0/+365
GChemPaint, a 2D chemical editor and some other programs related to chemistry suitable for the GNOME desktop. The Gnome Chemistry Utils include three utilities: - a 2D chemical editor (GChemPaint). - a chemical calculator (computes raw formule, molar weight, mass composition, etc..) and isotopic pattern). - a molecule 3d viewer using OpenGL to display molecular models. - a crystal structues viewer and editor. - a periodic table of the elements. - a spectrum viewer. These programs are based on an included C++ library which provides a few widgets and various classes, some related to chemistry and some utility classes.
2011-10-05Initial import of openbabel-2.3.0 from wip/openbabelryoon7-0/+338
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
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