Commit graph

58 commits

Author SHA1 Message Date
salo
d080980ff9 Fix thinko, /usr -> ${PREFIX}. 2002-12-01 20:25:39 +00:00
salo
c7a2c08d66 USE_PKGLOCALEDIR. 2002-11-30 15:31:59 +00:00
seb
1f825479a3 Use buildlink2. Use perl5/module.mk. 2002-10-27 22:51:06 +00:00
jlam
0c5b2825de buildlink1 -> buildlink2 2002-09-29 01:32:05 +00:00
jlam
48b937280b buildlink1 -> buildlink2 2002-09-21 01:23:56 +00:00
wiz
44c3d794a9 Standardize. 2002-09-12 17:05:15 +00:00
cjep
4214621b95 Small pkglint white-space complaint. 2002-06-07 11:34:40 +00:00
cjep
24c669225e Add NetBSD tags. 2002-05-20 17:25:43 +00:00
jtb
d342dc6405 Update to version 1.4.1. Numerous bug fixes since 1.3. 2002-05-03 22:03:08 +00:00
cjep
4719ab3423 Avoid egcs internal compiler error by using gcc-2.95.3 on arm32. 2002-04-20 14:41:05 +00:00
jmc
d0b4063d5a Include x11.buildlink.mk 2001-12-06 04:30:09 +00:00
jlam
96904a0049 Buildlinkify. 2001-11-28 05:20:38 +00:00
agc
be9bc4ff1b Replace "${GTAR} cf - . | (cd ... ; ${GTAR} xf - )" pipelines with a
single instance of ${PAX}.
2001-11-14 14:47:53 +00:00
zuntum
273821c4d3 Move pkg/ files into package's toplevel directory 2001-10-31 20:59:00 +00:00
agc
a16fc84f19 Deprecate NO_WRKSUBDIR, replacing it with an explicit assignment of:
WRKSRC= ${WRKDIR}

This is much cleaner, much more indicative of what happens, and removes
another of the negative definitions (NO_.* = value).
2001-09-09 20:36:07 +00:00
jlam
2c2b34a0f5 Remove explicit settings of FOO_CONFIG=${BUILDLINK_CONFIG_WRAPPER.foo} in
MAKE_ENV as they are now added by the buildlink files themselves.
2001-08-17 21:16:45 +00:00
jtb
afa3475a3e Update to 5.0.
Among the many changes:

*  New MPI version
*  Now uses autoconf/automake

See the ChangeLog for full details.
2001-07-08 13:36:33 +00:00
zuntum
d0e304aeaa Converted to use buildlink.mk 2001-06-30 11:56:20 +00:00
jtb
b97c41dde3 Remove redundant echoing, quoting, and input redirection to sed. 2001-04-28 23:59:17 +00:00
jtb
54656e7763 chemtool.1 is a leftover from the i386 bulk build. 2001-04-26 21:07:02 +00:00
agc
c180ae6ba2 move to sha digest, and add distfile size. 2001-04-19 16:12:32 +00:00
agc
b78848d6ca Move to sha1 digests, and add distfile sizes. 2001-04-19 16:02:23 +00:00
agc
18ea9c7e79 + move the distfile digest/checksum value from files/md5 to distinfo
+ move the patch digest/checksum values from files/patch-sum to distinfo
2001-04-17 10:22:24 +00:00
jtb
eb0cef2016 Change MAINTAINER section to packages@netbsd.org 2001-04-14 21:43:38 +00:00
jtb
ef5a1dd759 Updated to bioperl-0.7.0.
Revision history for Bioperl core modules

0.7  Large number of changes, including refactoring of the
     Object system, new parsers, new functionality and
     all round better system. Highlights are:


     o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
       Bio::Root::IO for I/O and file/handle capabilities.

     o Imported BPlite modules from Ian Korf for BLAST
       parsing. This is considered the supported BLAST parser;
       Bio::Tools::Blast.pm will eventually phase out due to lack of support.

     o Improved Sequence Feature model. Added complete location
       modelling (with fuzzy and compound locations).  See
       Bio::LocationI and the modules under Bio/Location.  Added
       support in Genbank/EMBL format parsing to completely parse
       feature tables for complex locations.

     o Moved special support for databanks etc to specialized modules under
       Bio/Seq/. One of these supports very large sequences through
       a temporary file as a backend.

     o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
       CDS retrieval and exon shuffling.

     o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF

     o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
       DB/GDB (the latter has platform-specific limitations).

     o New analysis parser framework for HT sequence annotation (see
       Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)

     o New Alignment IO framework

     o New Index modules (Swissprot)

     o New modules for running Blast within perl
       (Bio::Tools::Run::StandAloneBlast). Added modules for running
       Multiple Sequence Alignment tools ClustalW and TCoffee
       (Bio::Tools::Run::Alignment).

     o New Cookbook-style tutorial (see bptutorial.pl). Improved
       documentation across the package.

     o Much improved cross platform support. Many known incompatibilities
       have been fixed; however, NT and Mac do not work across the entire
       setup (see PLATFORMS).

     o Many bug fixes, code restructuring, etc. Overall stability and
       maintainability benefit a lot.

     o A total of 957 automatic tests


0.6.2

   There are very few functionality changes but a large
   number of software improvements/bug fixes across the package.

   o The EMBL/GenBank parsing are improved.

   o The Swissprot reading is improved. Swissprot writing
     is disabled as it doesn't work at all. This needs to
     wait for 0.7 release

   o BLAST reports with no hits are correctly parsed.

   o Several other bugs of the BLAST parser (regular expressions, ...)
     fixed.

   o Old syntax calls have been replaced with more modern syntax

   o Modules that did not work at all, in particular the Sim4
     set have been removed

   o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
     have improved compliance with interface specs and documentation

   o Mailing list documentation updated throughout the distribution

   o Most minor bug fixes have happened.

   o The scripts in /examples now work and have the modern syntax
     rather than the deprecated syntax


0.6.1  Sun April 2 2000

   o Sequences can have Sequence Features attached to them
        - The sequence features can be read from or written to
          EMBL and GenBank style flat files

   o Objects for Annotation, including References (but not
     full medline abstracts), Database links and Comments are
     provided

   o A Species object to represent nodes on a taxonomy tree
     is provided

   o The ability to parse HMMER and Sim4 output has been added

   o The Blast parsing has been improved, with better PSI-BLAST
     support and better overall behaviour.

   o Flat file indexed databases provide both random access
     and sequential access to their component sequences.

   o A CodonTable object has been written with all known
     CodonTables accessible.

   o A number of new lightweight analysis tools have been
     added, such as molecular weight determination.

    The 0.6 release also has improved software engineering

   o The sequence objects have been rewritten, providing more
     maintainable and easier to implement objects. These
     objects are backwardly compatible with the 0.05.1 objects

   o Many objects are defined in terms of interfaces and then
     a Perl implementation has been provided. The interfaces
     are found in the 'I' files (module names ending in 'I').

     This means that it is possible to wrap C/CORBA/SQL access
     as true "bioperl" objects, compatible with the rest of
     bioperl.

   o The SeqIO system has been overhauled to provide better
     processing and perl-like automatic interpretation of <>
     over arguments.

   o Many more tests have been added (a total of 172 automatic
     tests are now run before release).



0.05.1 Tue Jun 29 05:30:44 1999
        - Central distribution now requires Perl 5.004. This was
          done to get around 5.003-based problems in Bio/Index/*
          and SimpleAlign.
        - Various bug fixes in the Bio::Tools::Blast modules
          including better exception handling and PSI-Blast
          support. See Bio/Tools/Blast/CHANGES for more.
        - Fixed the Parse mechanism in Seq.pm to use readseq.
	  Follow the instructions in README for how to install
	  it (basically, you have to edit Parse.pm).
        - Improved documentation of Seq.pm, indicating where
          objects are returned and where strings are returned.
        - Fixed uninitialized warnings in Bio::Root::Object.pm
          and Bio::Tools::SeqPattern.pm.
        - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.

0.05  Sun Apr 25 01:14:11 1999
        - Bio::Tools::Blast modules have less memory problems
          and faster parsing. Webblast uses LWP and supports
          more functionality. See Bio/Tools/Blast/CHANGES for more.
        - The Bio::SeqIO system has been started, moving the
          sequence reformatting code out of the sequence object
        - The Bio::Index:: system has been started, providing
          generic index capabilities and specifically works for
          Fasta formatted databases and EMBL .dat formatted
	  databases
        - The Bio::DB:: system started, providing access to
          databases, both via flat file + index (see above) and
          via http to NCBI
        - The scripts/ directory, where industrial strength scripts
          are put has been started.
        - Many changes - a better distribution all round.
2001-04-05 21:48:40 +00:00
zuntum
4cb05636c7 Fix quoting 2001-04-01 11:06:30 +00:00
jtb
10e5a9abde Use ${PKGLOCALEDIR}. 2001-03-04 17:33:42 +00:00
wiz
79a4bfc219 Not needed any more -- COMMENTs are in Makefiles now. 2001-02-16 15:52:49 +00:00
wiz
02e8ee6a47 Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT.
While I'm here, unify category Makefiles to more standard style.
(If you have tools depending on the previous form, please fix them.)
2001-02-16 15:51:46 +00:00
wiz
2db9056f6e Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT. 2001-02-16 13:41:26 +00:00
jtb
d11401208b It appears that the source has moved. Fixes i386 bulk build problem. 2001-02-15 16:09:55 +00:00
jtb
0384ee5674 Updated chemtool to 1.3. Changes:
1.3a1	Fixed and restored XBM export. Added a (almost empty) template menu
	(the beginnings of which were already hidden in 1.2a8). Fixed kerning
	of mixed sub- and superscripts (as in SO_4^2^-). Changed allocation of
	initial drawing area, calculate actual size before saving.
1.3a2	Added option menu for default bond type , added label support to
	template function
1.3a3   Reduced preallocated drawing area to 'windowsize+100', as the increase
	in 1.3a1 (which used window+1000) caused a massive slowdown at startup.
        Freed unneeded pixmaps in the button setup code.
        Fragment rotation code now stores the initial coordinates and uses them
        as basis for the new positions - the previous, incremental calculation
        was severely plagued by accumulation of errors.
1.3a4	Changed bond option menu to use small icons instead of longer and less
	clear text labels. Removed check for 'cursor inside marked region' in
	'Move' mode to allow smooth dragging. Started populating the O and N
	heterocycle panels of the template menu. Fixed a duplicate bond in the
	tcdd example, and removed those examples that have become templates.
1.3a5	Added shortcut for some labels - pressing c,n,o,s,p,r,i,h,d or b
	inserts the corresponding centered element symbol at the last
	drawing position, 'l','1','2','3' insert the left justified labels
	'Cl','CH','CH_2','CH_3'. Fixed a GC leak in export_bitmap.
1.3a6   Moved the nucleoside examples to the template system. Made marker
	position default to last drawing position, so that the 'Add' function
	is now always active. Beginnings of internationalization (.mo file
	for German locale added). Fixed naphthalene template, added dicyclo-
	pentadiene. Changed Add_atom to automatically convert blanks in label
	input to backslashes for storage. Prepared a few drawings for later
	inclusion in the template system (camphor,pteridine,caffeine,glucose,
	fructose,mannose,galactose,neuraminic acid, spiro[4.5]decane).
1.3a7   Template cleanup: porphine moved to heterocycle panel, spirodecane
	added in its place. Glc,Fru,Man,Gal transfered to carbohydrate
	templates, caffeine to heterocycles. Czech translation (by Radek
	Liboska) added. Improved bounding box coordinates for xfig compound
	object (used for sub/superscripted labels) Changed export functions
	to remove the intermediate '.f2l' files. Changed orientation in xfig
	header to Portrait. Adapted xfig (and xfig-based) export modes to
	the new XFig default depth of 100. Changed depth of xfig text (labels)
	to 90 and added filled white polygons at depth 95 to hide overlapping
	line segments (experimental, used only for sub/superscripted text at
	the moment). Reset default filename to 'unnamed' when the current
	molecule is deleted.
1.3a8	Changed buttons mark/move/rotate/flip/delete/copy from text to icon
	to reclaim space for the text entry box (icons created by Radek
	Liboska). Added white polygon to clear area under normal text as well.
1.3a9	Added program icon. Added an interface for Radek Liboskas standalone
	program CHT, which calculates sum formula and molecular weight from
	a chemtool sketch. Corrected example drawing of brevetoxin.
1.3a10	Really reset mark flag when nothing was within the marker box.
	Allow saving only the marked region (formula weight computation only).
	Helper program CHT now parses those labels that are not in its
	internal table of common substituents; exact mass is now returned
	automatically.Added status line with message history.
1.3a11	Internationalization support made optional (define DISABLE_NLS in
	the Imakefile if you do not want it) to allow compiling on systems
	without GNU-style locale support again.
	Improved ring size and position in the benzene and cyclopentadiene
	templates (Michael Banck). Reset all marks before loading a template.
	If the template menu is already open, pressing the Template button now
	brings it to the front. Added templates (inden,biphenyl), removed the
	ugly question mark placeholders.
	Changed handling of windowmanager events, so that using the window
	decorations' CLOSE button brings up the Yes/No dialog while the
	chemtool window is still alive.
	Changes in helper program CHT (cht011a): now recognizes Ac in complex
	substituents; correctly handles aromatic 'ring' in formula input;
        checks input file for identifier "Chemtool"; reads number of bonds
	from "bonds" line (to handle label-only files gracefully); exits on
	unattached labels instead of silently miscalculating formula and
	mass. Subsequently updated to Radek Liboskas current version 0.19,
	which already includes equivalent changes. Added list of abbreviations
	supported by cht.
1.3a12	Reset all marks before 'adding' a sketch. Adding a label on top of an
	existing one now replaces the old label as it should. Added a function
	for rescaling objects (useful for drawing reagents above the reaction
	arrow - but labels are not rescaled yet). Added linetype 13, a single
	bond with opaque background (for crossing bonds - see the bicyclooctane
	template). Updated the German translation.
	This - plus or minus some templates - is my release candidate for 1.3.
1.3a13  Dropped the internal icon, as it was only causing trouble, especially
	with KDE. Most window managers allow specification of an external icon
	anyway (added chemtool.xpm for this purpose). Moved 'delete fragment'
	button to the end of the button row. Updated Czech translation by
	Radek Liboska. Added linetype 13 to the helper program CHT, made it
	accept any Chemtool 1.x file, not only version 1.2. Updated the
	'documentation', i.e. the README file, split out an INSTALL file. Set
	version number in chemtool files to 1.3. Fixed bug that left a newly
	'added' structure active but unable to move. Rewrote positioning
	logic for subscripts and right-justified text in export modes again.
	Changed screen display of molecule from 'fixed' fonts to helvetica
	as used in the export modes - previously, labels that appeared fine
	on screen could overlap in the final (postscript) output. Fixed
	'mannose' template that showed exactly this. Added formatting option
	'|' for slanted characters (as in iPr,tBu).
1.3a14  Fixed label shortcuts for CH_2 and CH_3 that could crash chemtool
	(buffer overrun). Fixed scaling in export function , which had been
	applied to labels only. Improved label size at smallest scale. Added
	correction factor for sub/superscript after certain characters (the joys
	of proportionally-spaced fonts :-( ). Handled reopening of template menu
	after a close via the window manager. Updated 'About' menu (mention Radek
	Liboska as developer, add the tu-darmstadt webpage).
1.3a15  Changed canvas bitmap allocation to avoid uncovering garbled portions
	when the sliders are used. Fixed fragment deletion code (deletion of
	the marked fragment and redisplay of the modified drawing are now
	performed immediately). This hopefully fixes the crashes some people
	have been seeing with this function.
1.3	Added Check for no (or no selected) atoms before trying to delete a
	fragment, fixed bug that could deletion of a fragment to fail.
	Changed functions for horizontal and vertical flip to transform the
	atom(s) directly bonded to the marked fragment as well. Added current
	filename (if any) to window title. Use xfig's own arrow type in export
	of regular arrows (Michael Banck).
	Some code cleanup: removed dead code, fixed unnecessary parameter
	passing between functions, tidied formatting with GNU indent. Removed
	Imakefile and provided regular Makefile (the build process relies on
	gtk-config, not xmkmf, since 1.2), added install targets for the
	localization files and manpage. Updated cht to version 1.3.
2001-02-12 02:16:02 +00:00
wiz
d4fce8d4e7 Unify format of MESSAGEs, and include RCS Ids. 2001-02-06 14:24:03 +00:00
jtb
43fc1ac0f0 Add and enable "chemtool". Fixes PR pkg/11377 by Jason Beegan. 2000-11-25 20:14:30 +00:00
jtb
39a4b46675 Initial import of new "chemtool" package:
Program for drawing organic molecules
2000-11-25 20:10:55 +00:00
agc
87cfcbbea9 Take advantage of bsd.prefs.mk - pointed out by IWAMOTO Toshihiro
Also convert some make(1) .for loops to sh(1) for loops.
2000-09-27 14:14:24 +00:00
jlam
18cba9d7fa Convert packages to use PERL5_PACKLIST (part 1). These were the easy
ones to do, and each compiled and installed/de-installed apparently
correctly.

As a side effect of the dynamic PLIST, we no longer need to have separate
-static and -shared PLISTs.  It's now easier than ever to make a perl5
package for NetBSD :)
2000-08-27 07:10:59 +00:00
jlam
bd206e6483 Correct unterminated cross-reference when building man pages. 2000-08-26 03:36:38 +00:00
hubertf
402899809a Replace MIRROR_DISTFILES and NO_CDROM with the more descriptive and
more fine-grained NO_{BIN,SRC}_ON_{FTP,CDROM} definitions.

MIRROR_DISTFILES and NO_CDROM are now dead.
2000-08-18 22:46:29 +00:00
wiz
18734b9939 add and enable rasmol 2000-03-13 04:43:21 +00:00
wiz
2a1d050c82 RasMol is a molecular graphics program intended for the visualisation of
proteins, nucleic acids and small molecules. The program is aimed at
display, teaching and generation of publication quality images.

Submitted by Marc Bauoin <babafou@babafou.eu.org> in pkg/8199, slightly
enhanced.
2000-03-13 04:41:58 +00:00
wiz
74874e66d9 remove trailing `.' 2000-03-09 13:47:31 +00:00
wiz
f895e15bb9 remove commented out SUBDIR += lines for packages that never got
converted from FreeBSD, or have been disabled since. Sorted lines
alphabetically, added some missing directories.
2000-02-25 01:04:11 +00:00
wiz
3a91bc506c remove trailing '.' 2000-02-05 18:18:14 +00:00
garbled
ca40abfb5a Initial import of nut program.
record what you eat and analyze your meals.
2000-01-11 02:56:33 +00:00
rh
1e10c515bb Add and enable fastDNAml 1999-07-28 20:20:39 +00:00
rh
5e8fd74d6c Import of fastDNAml-1.2.1, a program for estimating maximum likelihood
phylogenetic trees from nucleotide sequences, as submitted by Marc Baudoin,
thanks!
1999-07-28 20:18:55 +00:00
rh
3458de5977 Enable clustalw 1999-07-28 20:08:38 +00:00
rh
12c166c31a Import of clustalw-1.8, a general purpose multiple alignment program
for DNA or proteins.  This is a merge of the packages submitted in PRs
pkg/7075 by Brook Milligan and pkg/8094 by Marc Baudoin (with some minor
modifications), thanks!
1999-07-28 20:07:00 +00:00
rh
1ac6e360cd Import of phylip-3.573c, a Phylogeny Inference Package, as submitted by
Marc Baudoin, thanks!
1999-07-28 19:58:56 +00:00