freebsd-ports/biology/Makefile

# $FreeBSD$
#

    COMMENT = Biology

    SUBDIR += L-Breeder
    SUBDIR += act
    SUBDIR += ariadne
    SUBDIR += artemis
    SUBDIR += avida
    SUBDIR += babel
    SUBDIR += biojava
    SUBDIR += chemeq
    SUBDIR += clustalw
    SUBDIR += coalesce
    SUBDIR += crimap
    SUBDIR += deft
    SUBDIR += distribfold
    SUBDIR += dna-qc
    SUBDIR += emboss
    SUBDIR += fasta
    SUBDIR += fasta3
    SUBDIR += fastdnaml
    SUBDIR += flip
    SUBDIR += fluctuate
    SUBDIR += garlic
    SUBDIR += genpak
    SUBDIR += gff2ps
    SUBDIR += gperiodic
    SUBDIR += grappa
    SUBDIR += hmmer
    SUBDIR += kinemage
    SUBDIR += lamarc
    SUBDIR += libgenome
    SUBDIR += lsysexp
    SUBDIR += migrate
    SUBDIR += molden
    SUBDIR += mopac
    SUBDIR += nab
    SUBDIR += ncbi-toolkit
    SUBDIR += nclever
    SUBDIR += ortep3
    SUBDIR += p5-AcePerl
    SUBDIR += p5-bioperl
    SUBDIR += paml
    SUBDIR += phylip
    SUBDIR += platon
    SUBDIR += povchem
    SUBDIR += primer3
    SUBDIR += psi88
    SUBDIR += py-biopython
    SUBDIR += pymol
    SUBDIR += rasmol
    SUBDIR += recombine
    SUBDIR += ruby-bio
    SUBDIR += seaview
    SUBDIR += seqio
    SUBDIR += sim4
    SUBDIR += spdbv
    SUBDIR += tRNAscan-SE
    SUBDIR += t_coffee
    SUBDIR += tinker
    SUBDIR += treepuzzle
    SUBDIR += treeviewx
    SUBDIR += wise
    SUBDIR += xdrawchem
    SUBDIR += xmolwt

.include <bsd.port.subdir.mk>
Change Id->FreeBSD. 1999-08-25 00:58:03 -04:00			`# $FreeBSD$`
The new ports category "biology" starts here today. No Darwin jokes please! 1997-12-13 00:54:24 -05:00			`#`

Remove category pkg/COMMENT files in favour of a COMMENT variable in the category makefile. Submitted by: Matthew Seaman <m.seaman@infracaninophile.co.uk> PR: 59651 2004-04-02 02:29:48 -05:00			`COMMENT = Biology`

New port L-Breeder version 1.0: Allows you to display and breed L-system forms PR: 38725 Submitted by: David Yeske <dyeske@yahoo.com> 2002-08-20 20:01:59 -04:00			`SUBDIR += L-Breeder`
New Port: biology/act PR: ports/35753 Submitted by: Camson Huynh <chuynh@biolateral.com.au> 2003-01-16 09:22:59 -05:00			`SUBDIR += act`
Add ariadne 1.3, programs to compare protein sequences and profiles, using the Smith-Waterman algorithm. PR: ports/67811 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> 2004-06-22 10:29:59 -04:00			`SUBDIR += ariadne`
Initial import of artemis 4.0 Artemis is a DNA sequence viewer and annotation tool. PR: 32914 Submitted by: Camson <chuynh@biolateral.com.au> 2001-12-22 09:39:40 -05:00			`SUBDIR += artemis`
add avida 1.6.0 Avida is an auto-adaptive genetic system designed for ALife research PR: 37268 Submitted by: Jeremy Karlson <karlj000@unbc.ca> 2002-04-20 11:17:46 -04:00			`SUBDIR += avida`
Activate babel. 1997-12-21 16:58:57 -05:00			`SUBDIR += babel`
Initial import of biology/biojava PR: 21678 Submitted by: Brad Chapman <chapmanb@arches.uga.edu> 2000-10-10 07:14:03 -04:00			`SUBDIR += biojava`
Activating the chemeq, clustalw, paml, and phylip ports. 2000-07-09 23:26:57 -04:00			`SUBDIR += chemeq`
			`SUBDIR += clustalw`
Add coalesce 1.50, a program to fit population models. 2001-08-06 10:41:58 -04:00			`SUBDIR += coalesce`
Add crimap 2.4, a tool for the creation of multilocus linkage maps. PR: 35198 Submitted by: Tony Maher <tonym@biolateral.com.au> 2002-03-27 09:42:56 -05:00			`SUBDIR += crimap`
Added deft and ortep3 1999-05-19 09:38:46 -04:00			`SUBDIR += deft`
Connect distribfold to build after moving it from misc category Prompted by: kris, Adam Weinberger <adam@vectors.cx>, Fernan Aguero <fernan@iib.unsam.edu.ar>, others 2002-10-06 23:07:59 -04:00			`SUBDIR += distribfold`
Add dna-qc 1993.07.26, a quality control algorithm for DNA sequencing projects. PR: 32998 Submitted by: Tony Maher <tonym@biolateral.com.au> 2001-12-18 22:20:48 -05:00			`SUBDIR += dna-qc`
Add emboss, the European Molecular Biology Open Software Suite PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com> 2000-07-31 15:13:54 -04:00			`SUBDIR += emboss`
New port: biology/fasta, the FASTA2 suite of DNA and protein sequence search tools PR: 24715 Submitted by: Johann Visagie <johann@egenetics.com> 2001-02-11 11:24:18 -05:00			`SUBDIR += fasta`
- New port: biology/fasta3, which comprises the FASTA3 suite of DNA and protein sequence search programs - FASTA3 updates only some of the elements of FASTA2, which is why I have submitted ports of both versions (as biology/fasta and biology/fasta3) PR: 24716 Submitted by: Johann Visagie <johann@egenetics.com> 2001-02-11 11:28:59 -05:00			`SUBDIR += fasta3`
Initial import of fastDNAml Version 1.2.2 The faster variant of DNAML, makes phylogenetic trees using maximum likelihood PR: 21931 Submitted by: Motomichi Matsuzaki <mzaki@e-mail.ne.jp> 2000-10-12 08:31:13 -04:00			`SUBDIR += fastdnaml`
Flip is used to find/translate orfs. WWW: ftp://megasun.bch.umontreal.ca/pub/flip/ PR: 35332 Submitted by: tonym@biolateral.com.au 2002-09-10 10:04:06 -04:00			`SUBDIR += flip`
Add fluctuate 1.30, a program to fit population models. 2001-08-06 10:45:39 -04:00			`SUBDIR += fluctuate`
A new port garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule. 2003-07-28 02:38:37 -04:00			`SUBDIR += garlic`
reimport biology/genpak 2001-02-27 21:46:51 -05:00			`SUBDIR += genpak`
Add gff2ps 0.97b, converts gff-formated genomic data-sets to PostScript. PR: 32920 Submitted by: Camson Huynh <chuynh@biolateral.com.au> 2001-12-19 05:03:26 -05:00			`SUBDIR += gff2ps`
Added gperiodic and xmolwt 1999-09-06 16:09:12 -04:00			`SUBDIR += gperiodic`
Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogeny Software. PR: 28541 Submitted by: dbader@eece.unm.edu 2001-07-04 04:39:40 -04:00			`SUBDIR += grappa`
Turn on hmmer. 1998-07-12 19:30:50 -04:00			`SUBDIR += hmmer`
Activate kinemage 1998-01-29 12:25:59 -05:00			`SUBDIR += kinemage`
Add lamarc 2001.08.06, a package of programs for computing population parameters. 2001-08-07 04:17:58 -04:00			`SUBDIR += lamarc`
add libgenome 0.5.0 Toolkit for developing bioinformatic related software in C++ 2002-07-30 06:57:06 -04:00			`SUBDIR += libgenome`
new port:biology/lsysexp L-system Explorer is a program used for viewing and creating L-system fractals. The following features are supported: - Over 500 builtin L-systems, arranged into about 20 groups. - Ability to create and save custom L-systems and L-system groups. - Abilty to save images of L-systems (in PNG or JPEG format). - Multiple L-systems can be viewed at the same time. - Able to use custom colors and gradients. - Can also generate random gradients, or completely random colors. - Able to draw using lines, points, or a random combination of both. PR: iports/51400 Submitted by: David Yeske <dyeske@yahoo.com> 2003-09-02 22:23:23 -04:00			`SUBDIR += lsysexp`
Add migrate 1.2, a program to estimate population sizes and migration rates. 2001-08-06 09:07:46 -04:00			`SUBDIR += migrate`
Add platon and molden 1999-05-07 02:59:25 -04:00			`SUBDIR += molden`
Add mopac and psi88 (Move mopac and psi88 from misc to biology) 1999-05-06 04:18:35 -04:00			`SUBDIR += mopac`
This is nab (nucleic acid builder), a language for macromolecules PR: 21585 Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU> 2000-10-09 22:56:57 -04:00			`SUBDIR += nab`
New Port: biology/ncbi-toolkit National Center for Biotechnology Information (NCBI) Development Toolkit. PR: 22388 Submitted by: Tony Maher <tony.maher@ebioinformatics.com> 2000-10-29 08:56:24 -05:00			`SUBDIR += ncbi-toolkit`
Add nclever 4.0, a character-based version of NCBI's Entrez program. PR: 30783 Submitted by: Tony Maher <tonym@biolateral.com.au> 2001-09-26 05:22:02 -04:00			`SUBDIR += nclever`
Added deft and ortep3 1999-05-19 09:38:46 -04:00			`SUBDIR += ortep3`
Add p5-AcePerl, a perl interface to the ACEDB genome database system PR: ports/20223 Submitted by: Johann Visagie <johann@egenetics.com> 2000-07-28 09:16:10 -04:00			`SUBDIR += p5-AcePerl`
Add BioPerl, a collection of Perl5 mods for bioinformatics/genomics PR: ports/20252 Submitted by: Johann Visagie <johann@egenetics.com> 2000-07-28 10:06:03 -04:00			`SUBDIR += p5-bioperl`
Activating the chemeq, clustalw, paml, and phylip ports. 2000-07-09 23:26:57 -04:00			`SUBDIR += paml`
			`SUBDIR += phylip`
Add platon and molden 1999-05-07 02:59:25 -04:00			`SUBDIR += platon`
Activate povchem. 1998-03-16 02:01:32 -05:00			`SUBDIR += povchem`
add primer3 0.9 Primer3 helps to choose primers for PCR reactions PR: 35298 Submitted by: Tony Maher <tonym@biolateral.com.au> 2002-09-17 11:31:09 -04:00			`SUBDIR += primer3`
Add mopac and psi88 (Move mopac and psi88 from misc to biology) 1999-05-06 04:18:35 -04:00			`SUBDIR += psi88`
Add py-biopython, is a collection of Python packages and modules created by the Biopython Project, intended to provide the basis for building bioinformatics applications in the Python language. PR: ports/20260 Submitted by: Johann Visagie <johann@egenetics.com> 2000-07-31 08:12:24 -04:00			`SUBDIR += py-biopython`
Add pymol 0.82, Free and Open-Source molecular modeling system. PR: 40694 Submitted by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp> 2002-08-13 07:53:43 -04:00			`SUBDIR += pymol`
Activate rasmol. 1997-12-15 12:47:41 -05:00			`SUBDIR += rasmol`
Add recombine 1.40, a program to fit population models across sites. 2001-08-06 10:49:53 -04:00			`SUBDIR += recombine`
Add ruby-bio (BioRuby), an integrated environment for Bioinformatics written in Ruby. 2001-10-24 02:21:52 -04:00			`SUBDIR += ruby-bio`
Activate seaview. 1997-12-21 17:05:43 -05:00			`SUBDIR += seaview`
Add seqio 1.2.2, a set of C functions which can read/write biological sequence files. PR: 29922 Submitted by: Tony Maher <tonym@biolateral.com.au> 2001-08-22 08:07:26 -04:00			`SUBDIR += seqio`
Add sim4, an implementation of the sim4 algorithm for aligning expressed DNA with genomic sequences PR: ports/20219 Submitted by: Johann Visagie <johann@egenetics.com> 2000-07-27 10:33:00 -04:00			`SUBDIR += sim4`
Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated homology modelling server developped at Glaxo Welcome Experimental Research in Geneva. Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain packing. Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modelling tools are integrated and command files for popular energy minimisation packages can be generated. Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images. WWW: http://www.expasy.ch/spdbv/ PR: 33902 Submitted by: chuynh@biolateral.com.au 2002-04-02 11:18:53 -05:00			`SUBDIR += spdbv`
Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection. PR: 33853 Submitted by: chuynh@biolateral.com.au 2002-03-27 09:18:49 -05:00			`SUBDIR += tRNAscan-SE`
Add t_coffee 1.37, a multiple DNA or protein sequence alignment package. 2002-01-25 09:58:16 -05:00			`SUBDIR += t_coffee`
Activate tinker. 1998-11-16 23:54:28 -05:00			`SUBDIR += tinker`
add treepuzzle 5.1 Maximum likelihood phylogeny reconstruction using quartets PR: 45241 Submitted by: Jan Lentfer <lentferj@neslonek.bio.tu-darmstadt.de> 2002-11-20 03:54:10 -05:00			`SUBDIR += treepuzzle`
Add treeviewx 0.1.1, a phylogenetic tree viewer. PR: 29770 Submitted by: Tony Maher <tonym@biolateral.com.au> 2001-08-17 04:39:28 -04:00			`SUBDIR += treeviewx`
"Wise2 is package that is focused on comparing DNA sequences at the level of its conceptual translation, regardless of sequencing error and introns." 2002-09-10 09:58:40 -04:00			`SUBDIR += wise`
Add xdrawchem 0.82 - a program for drawing molecules 2000-07-19 09:23:02 -04:00			`SUBDIR += xdrawchem`
Added gperiodic and xmolwt 1999-09-06 16:09:12 -04:00			`SUBDIR += xmolwt`
The new ports category "biology" starts here today. No Darwin jokes please! 1997-12-13 00:54:24 -05:00
			`.include <bsd.port.subdir.mk>`