Commit graph

135 commits

Author SHA1 Message Date
ben
bbbcaa8abd Modify patch-aa to replace -e tests with -d tests, so install will work
on IRIX.  Addresses PR#26647.
2004-08-23 14:41:06 +00:00
ben
5c410f3331 Remove unnecessary -p following MKDIR commands. 2004-08-23 14:37:04 +00:00
ben
5d93b3b69b Fix patch-aa so gp installs under IRIX. Addresses PR#26647.
Patch supplied by Georg Schwarz.
2004-08-19 16:55:31 +00:00
ben
72d33fb01b Update to glimmer-2.13, thanks to cngo@nmsu.edu.
CHANGELOG, 12 October 2003
    add -X option to glimmer2, to allow orfs extending off ends of
    sequence to be scored.  Also fix bug affecting -p and -o options
    when user chose zero overlap.
2004-08-19 16:47:01 +00:00
wiz
5eeee836c2 Update to 10.2:
This release fixes a computation error in the value for monounsaturated fat
when the user sets a fat level higher than the Daily Value.
2004-08-18 11:22:36 +00:00
ben
16e195c46d Add DIST_SUBDIR because contents changed while archive filename did not. 2004-08-17 02:48:04 +00:00
ben
ee36ecf16f Update phylip to version 3.61. No ChangeLog included. However there is a
very long list of bux fixes since 3.57 at:
http://evolution.genetics.washington.edu/phylip/bugs.html
2004-08-16 23:58:35 +00:00
ben
d019d671d6 Update fastDNAml to version 1.2.2. Notable changes include:
* Now under GPL
* Convert to function definitions with parameter type lists
* General code clean-up
2004-08-16 23:45:59 +00:00
ben
7bf8866f8c Update to clustalw 1.83. Changes since 1.8 include:
* The FASTA format has been added to the list of alignment output
options.

* It is now possible to save the residue ranges (appended after the
sequence names) when saving a specified range of the alignment.

* The efficiency of  the neighour-joining algorithm has been improved.
This work was done by Tadashi Koike at the Center for Information
Biology and DNA Data Bank of Japan and FUJITSU Limited.

Some example speedups are given below : (timings on a SPARC64 CPU)

No. of sequences        original NJ     new NJ
     200                0' 12"          0.1"
     500                9' 19"          1.4"
     1000               XXXX            0' 31"

* ClustalW now returns error codes for some common errors when exiting.
This may be useful for people who run clustalw automatically from within
a script.
Error codes are:
	1	bad command line option
	2	cannot open sequence file
	3	wrong format in sequence file
	4	sequence file contains only 1 sequence (for multiple
		alignments)

* Alignments can now be saved in Nexus format, for compatibility with
PAUP, MacClade etc. For a description of the Nexus format, see:
Maddison, D. R., D. L. Swofford and W. P. Maddison.  1997.
NEXUS: an extensible file format for systematic information.
Systematic Biology 46:590-621.

* Phylogenetic trees can also be saved in nexus format.

* A ClustalW icon has been designed for MAC and PC systems.
2004-08-16 23:34:58 +00:00
ben
3a9380afa6 Make hmmer honor $MKDIR for cross-platform install.
Addresses pr#26650 from Georg Schwarz.
2004-08-16 02:47:49 +00:00
ben
3f14829dd3 Update HOMEPAGE, addresses PR#26667 from Georg Schwarz. 2004-08-15 13:37:24 +00:00
wiz
d147c8fb22 Update to 10.1:
10.1:
This release adds a fix for zero values that display as no data.
10.0:
This release updates the USDA Nutrient Database to version SR17, and allows
current NUT installations to have their existing meal records reinterpreted
with the new database.
9.20:
This release optimizes the new code of the last release, the focus of which
was distinguishing no data from zero in the USDA database.
9.19:
The program now distinguishes between zero values and no data in the USDA
database, and uses this information to produce a new screen that lists foods
high in some nutrient while minimizing some other nutrient.
9.18:
This release contains revisions to the polyunsaturated fatty acid reference
values and how they scale up as fats increase and carbs decrease.
9.17:
This release provides what may be more reasonable or optimal default settings
for fat percentages when the user sets the program for low carb.
9.16:
This release contains bugfixes for a segmentation fault which occurred when
entering a control-D and a monounsaturated fat reference value that was too
high.
9.15:
This release makes serving sizes more consistent among food groups. It adds
functions to change the default serving size, and to sort foods by nutrients
per serving.
9.14:
This release adds support for an optional database subdirectory, allowing the
user to easily maintain multiple databases, for multiple family members, for
instance. It also adds display of non-fiber carbohydrate grams ("net carbs")
on the main analysis screen.
9.13:
The program now allows commercial foods that have a nutrition label and an
ordered ingredients statement to be added to the food database. An
approximation to a food's recipe is found that best fits the criteria and the
recipe is analyzed to provide information about the additional nutrients not
stated on the nutrition label.
9.12:
[unknown]
2004-08-15 12:06:34 +00:00
ben
cc21249d64 Update HOMEPAGE and MASTER_SITES to new locations.
Update distinfo for new archive.  Only minor bug fixes, no version change.
For a detailed diff, see:
ftp://ftp.netbsd.org/pub/NetBSD/misc/ben/profit-2004-08-14.txt

This addresses PR#26656 from Georg Schwarz.
2004-08-14 20:52:09 +00:00
snj
9791cde6d6 Use buildlink3. Requested by Georg Schwarz in PR pkg/26654. 2004-08-14 15:51:37 +00:00
grant
0503e60527 don't call "install -d" with multiple directory arguments. 2004-06-11 13:22:36 +00:00
snj
74367fe413 Convert to buildlink3. 2004-04-11 04:07:05 +00:00
snj
7b4bd4a804 Convert to buildlink3 and correct a spelling error in DESCR. 2004-04-11 04:06:09 +00:00
snj
847fda614b Convert to buildlink3. 2004-04-11 03:50:56 +00:00
minskim
03a3e5f9a4 bl3ify and enable pkgviews installation. 2004-04-10 02:40:01 +00:00
minskim
76c9962543 Disable gnome support explicitly. Otherwise this package installs
more files on platforms where /usr/share/mime-info exists.
2004-04-10 02:33:12 +00:00
wiz
7e32f9de41 Update to 9.11:
New in 9.11:
Because the program uses the approximation of 4 calories per gram
for carbohydrate and protein to analyze meals according to the
"Daily Value" -- although real food has various values for calories
per gram -- the program now refigures fat percentage values at each
analysis so that when calories, carbs, and protein are each at
exactly 100%, fat will be also.
New in 9.10:
This release fixes a buffer overflow in the food selection function
which caused the program to not find certain foods even though they
existed in the database.
New in 9.9:
A bug has been fixed in which during food selection, the program
lost the value of the food name key. Also, some of the program's
reference values for the essential fatty acids have been modified.
New in 9.8:
The program now defaults to either grams or ounces, depending on
the weight unit the user enters to specify servings. A bug in
handling customary meal names that are too long has been fixed.
New in 9.7:
The program computes essential fatty acid reference values based
on the user's diet. Prior releases aimed toward a particular balance
of Omega-6 and Omega-3. This release allows the user to specify
the balance between Omega-6 and Omega-3 without having to determine
the amount of the individual fatty acids.
New in 9.6:
The program is now capable of understanding food names in simple
English, such as "fried chicken" and "mashed potatoes." This is
accomplished by including the list of abbreviations the USDA uses
and by successively searching for each tokenized term, whatever
the order in the USDA name.
2004-03-10 18:37:48 +00:00
minskim
13da5d6ea6 Do not install files not specified in PLIST.
While here, remove trailing whitespace and enable pkgviews installation.
2004-02-18 21:13:48 +00:00
jlam
3ac2d4b8aa In the new compiler selection framework, GCC_REQD is appended to, not
overridden.
2004-02-01 01:43:28 +00:00
grant
b2d1f41ee2 call ${MAKE} with the right environment and arguments, override CC.
fixes build with non-gcc.

minor style fixes.
2004-01-29 13:41:05 +00:00
grant
0fe93082c3 make sure we use ${CC}. 2004-01-29 13:34:24 +00:00
kristerw
03e47212a7 Use GCC_REQD instead of USE_PKGSRC_GCC when overriding the compiler
for arm, so that we don't need to install the gcc package(s) on
machines that already have a working compiler in their /usr/bin.
2004-01-24 20:55:42 +00:00
grant
ed16993a08 replace deprecated USE_GMAKE with USE_GNU_TOOLS+=make. 2004-01-22 07:14:59 +00:00
agc
dc52048e01 Move WRKSRC definition away from the first paragraph in a Makefile. 2004-01-20 12:07:06 +00:00
cjep
ae7fd52e7b Add trailing / on HOMEPAGEs 2003-12-30 17:21:54 +00:00
wiz
0989e29e4b Update to 9.5:
9.5:
The last release introduced a bug when adding customary meals to
regular meals. The program now adds the foods without the additional
prompt screen.
9.4:
This release changes the method of searching for foods to a substring
search. The narrowing-down of food categories to a unique food is
the same as in prior releases.
2003-12-25 14:46:17 +00:00
wiz
08e57f51e7 Update to 9.3:
This release fixes a bug in the graphs where the "Daily Value" was
such a small percentage of the values graphed that the DV line
indicator exceeded the graph width.
2003-12-13 10:44:06 +00:00
jschauma
7e5f7ad7b8 Apply patches from Tyler Retzlaff in PR pkg/23083 to make this behave with
gcc3.  While here, update to version 2.12 (previous version was erraneously
named 2.1, when it should have been 2.10) which is the only distfile
available on the ftp site.
Changelog seems to say:
   - Fix bug on long-orfs.cc to avoid occasional array out-of-bounds
	error (detected on Mac OS X).
2003-10-07 18:20:15 +00:00
wiz
2577cc71b7 Update to 9.2:
9.2:
The upper limit of the polyunsaturated reference value for linoleic
acid has been reduced to 4% of calories, while that for alpha
linolenic acid has been raised to 2%. An internal constant for the
percentage of total fat that is fatty acids has been replaced by
a function that figures it for each analysis.

9.1:
The program is no longer limited to three meals a day, and can now
be set for 1 to 19 meals per day. A list of the meals not yet
recorded for a selected day is displayed as a mnemonic during the
"Record Meals" function.
2003-10-05 10:24:57 +00:00
jschauma
3e0bfff865 Add/enable xylem 2003-10-04 19:16:29 +00:00
jschauma
558f18b319 Initial import of xylem, one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.

XYLEM is a package of tools designed to exploit the Unix environment to enable
the user to identify, extract and manipulate data from major databases such as
GenBank, EMBL and PIR.
2003-10-04 19:13:28 +00:00
jschauma
c34937f178 Add/enable glimmer. 2003-09-30 02:11:32 +00:00
jschauma
b92c4d6b4b Initial import of glimmer, one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.

Glimmer (Gene Locator and Interpolated Markov Modeler) is a system for finding
genes in microbial DNA, especially the genomes of bacteria and archaea.
Glimmer uses interpolated Markov models (IMMs) to identify the coding regions
and  distinguish them from noncoding DNA. The IMM approach uses a combination
of Markov models from 1st through 8th-order, weighting each model according to
its predictive power.
2003-09-30 02:11:06 +00:00
jschauma
ecaefb1578 Add/enable genesplicer. 2003-09-30 01:57:35 +00:00
jschauma
f4364c13ef Initial import of genesplicer, one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.

GeneSplicer is a  fast, flexible system for detecting splice sites in the
genomic DNA of various eukaryotes. The system has been trained and tested
successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human,
Drosophila, and rice.
2003-09-30 01:57:08 +00:00
jschauma
53f2681a9f Add/enable fluctuate. 2003-09-30 01:20:02 +00:00
jschauma
487853693e Initial import of fluctuate, one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.

FLUCTUATE fits the model which has a single population which has been
growing (or shrinking) according to an exponential growth law. It
estimates 4Nu and g, where N is the effective population size, u is
the neutral mutation rate per site, and g is the growth rate of the
population.
2003-09-30 01:19:31 +00:00
jschauma
f04d4bf38a Add/enable coalesce. 2003-09-30 01:04:39 +00:00
jschauma
ed400565a2 Initial import of coalesce, one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.

COALESCE fits the model which has a single population of constant size, and
estimates 4Nu, where N is the effective population size and u is the neutral
mutation rate per site.
2003-09-30 01:03:56 +00:00
jschauma
52e686b5bd Add/enable stride 2003-09-27 23:47:20 +00:00
jschauma
d844618851 Initial import of stride, one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.

Knowledge-based protein secondary structure assignment from atomic
coordinates.
2003-09-27 23:46:55 +00:00
jschauma
7b86174cc4 Add/enable sewer 2003-09-27 23:36:59 +00:00
jschauma
a328110a95 Initial import of sewer, one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.

SeWeR is SEquence Analysis using WEb Resources. It has web based Sequence
Analysis. SeWeR is an integrated portal to common web-based services in
bioinformatics.
2003-09-27 23:36:34 +00:00
jschauma
115d93fc1f Add/enable profit 2003-09-27 23:18:55 +00:00
jschauma
b1ac371053 Initial import of profit, one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.

ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate
program for performing least squares fits of two protein structures. It
performs a very simple and basic function, but allows as much flexibility as
possible in performing this procedure. Thus one can specify subsets of atoms
to be considered, specify zones to be fitted by number, sequence, or by
sequence alignment.
2003-09-27 23:18:26 +00:00
jschauma
17127b1ec0 Add/enable mummer 2003-09-27 22:25:54 +00:00