freebsd-ports/biology/Makefile

# $FreeBSD$
#

    COMMENT = Biology

    SUBDIR += L-Breeder
    SUBDIR += adun
    SUBDIR += ariadne
    SUBDIR += artemis
    SUBDIR += avida
    SUBDIR += babel
    SUBDIR += belvu
    SUBDIR += biococoa
    SUBDIR += biojava
    SUBDIR += blast
    SUBDIR += blat
    SUBDIR += boinc-simap
    SUBDIR += chemeq
    SUBDIR += clustalw
    SUBDIR += crimap
    SUBDIR += distribfold
    SUBDIR += dna-qc
    SUBDIR += dotter
    SUBDIR += embassy
    SUBDIR += emboss
    SUBDIR += fasta
    SUBDIR += fasta3
    SUBDIR += fastdnaml
    SUBDIR += finchtv
    SUBDIR += fluctuate
    SUBDIR += garlic
    SUBDIR += genpak
    SUBDIR += gff2ps
    SUBDIR += gmap
    SUBDIR += gperiodic
    SUBDIR += grappa
    SUBDIR += hmmer
    SUBDIR += jalview
    SUBDIR += kinemage
    SUBDIR += lagan
    SUBDIR += lamarc
    SUBDIR += libgenome
    SUBDIR += linux-foldingathome
    SUBDIR += lsysexp
    SUBDIR += mafft
    SUBDIR += migrate
    SUBDIR += molden
    SUBDIR += mopac
    SUBDIR += mrbayes
    SUBDIR += mummer
    SUBDIR += nab
    SUBDIR += ncbi-toolkit
    SUBDIR += ortep3
    SUBDIR += p5-AcePerl
    SUBDIR += p5-Bio-ASN1-EntrezGene
    SUBDIR += p5-Bio-Das
    SUBDIR += p5-Bio-Phylo
    SUBDIR += p5-bioperl
    SUBDIR += p5-bioperl-devel
    SUBDIR += p5-bioperl-run
    SUBDIR += p5-bioperl-run-devel
    SUBDIR += paml
    SUBDIR += phylip
    SUBDIR += platon
    SUBDIR += povchem
    SUBDIR += primer3
    SUBDIR += protomol
    SUBDIR += psi88
    SUBDIR += py-biopython
    SUBDIR += pymol
    SUBDIR += rasmol
    SUBDIR += recombine
    SUBDIR += ruby-bio
    SUBDIR += seaview
    SUBDIR += seqio
    SUBDIR += sim4
    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 06:58:03 +02:00			`# $FreeBSD$`
The new ports category "biology" starts here today. No Darwin jokes please! 1997-12-13 06:54:24 +01:00			`#`

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 09:29:48 +02:00			`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> 2002-08-21 02:01:59 +02:00			`SUBDIR += L-Breeder`
Adun is a new extendible molecular simulation program that also includes data management and analysis capabilities. WWW: http://diana.imim.es/Adun Submitted by: Gürkan Sengün Reviewed by: dinoex 2006-11-09 21:16:54 +01:00			`SUBDIR += adun`
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 16:29:59 +02:00			`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 15:39:40 +01:00			`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 17:17:46 +02:00			`SUBDIR += avida`
Activate babel. 1997-12-21 22:58:57 +01:00			`SUBDIR += babel`
Add belvu 2.29, a viewer for multiple sequence alignments. PR: ports/93056 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> 2006-03-15 11:24:57 +01:00			`SUBDIR += belvu`
The BioCocoa framework provides developers with the opportunity to add support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE, Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and TNT files by writing only three lines of code. The framework is written in Cocoa (Objective-C). WWW: http://bioinformatics.org/biococoa/ 2006-12-30 10:20:54 +01:00			`SUBDIR += biococoa`
Initial import of biology/biojava PR: 21678 Submitted by: Brad Chapman <chapmanb@arches.uga.edu> 2000-10-10 13:14:03 +02:00			`SUBDIR += biojava`
Add blast, a powerful software package for gene and protein identification, using sensitive, selective and rapid similarity searches of protein and nucleotide sequence databases. PR: ports/69636 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> 2004-11-11 22:35:04 +01:00			`SUBDIR += blast`
Add blat 33, a fast tool for local sequence similarity searches. PR: ports/93060 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> 2006-03-15 11:26:12 +01:00			`SUBDIR += blat`
- Sort category Makefiles Inspired by: Jason Harris <jharris@widomaker.com> Howto: http://twiki.cenkes.org/Cenkes/SortingCategoryMakefiles 2007-10-06 01:33:27 +02:00			`SUBDIR += boinc-simap`
- Resurrect, update to version 1.5 (literally 1.50 since I wanted to avoid unnecessary PORTEPOCH bump) - Update MASTER_SITES and WWW line, provide backup download site - Come up with better port description - Reset maintainer to ports@ - Uphold CXX and CXXFLAGS - Clean up Makefile slightly - Don't install yet another copy of GPL and texts in French - Add SHA256 hash to distinfo 2006-01-19 20:47:59 +01:00			`SUBDIR += chemeq`
- Sort category Makefiles Inspired by: Jason Harris <jharris@widomaker.com> Howto: http://twiki.cenkes.org/Cenkes/SortingCategoryMakefiles 2007-10-06 01:33:27 +02:00			`SUBDIR += clustalw`
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 15:42:56 +01:00			`SUBDIR += crimap`
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 2002-10-07 05:07:59 +02:00			`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> 2001-12-19 04:20:48 +01:00			`SUBDIR += dna-qc`
Add dotter 20021204 # last modified date in FTP server, a viewer for multiple sequence alignments. PR: ports/93055 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> 2006-03-15 11:35:24 +01:00			`SUBDIR += dotter`
[new port] biology/embassy PR: ports/74330 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar> 2004-11-26 17:34:22 +01:00			`SUBDIR += embassy`
Add emboss, the European Molecular Biology Open Software Suite PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com> 2000-07-31 21:13:54 +02:00			`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 17:24:18 +01:00			`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 17:28:59 +01:00			`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 14:31:13 +02:00			`SUBDIR += fastdnaml`
Add finchtv 1.3.0, a chromatogram trace viewer. PR: 70271 Submitted by: Fernan Aguero <fernan (at) iib.unsam.edu.ar> 2005-03-11 22:16:16 +01:00			`SUBDIR += finchtv`
Add fluctuate 1.30, a program to fit population models. 2001-08-06 16:45:39 +02:00			`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 08:38:37 +02:00			`SUBDIR += garlic`
reimport biology/genpak 2001-02-28 03:46:51 +01:00			`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 11:03:26 +01:00			`SUBDIR += gff2ps`
Add gmap 2006.04.21, a Genomic Mapping and Alignment Program for mRNA and EST Sequences. PR: ports/103651 Submitted by: Bob Zimmermann <rpz at cse.wustl.edu> 2006-09-29 06:05:55 +02:00			`SUBDIR += gmap`
Added gperiodic and xmolwt 1999-09-06 22:09:12 +02:00			`SUBDIR += gperiodic`
Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogeny Software. PR: 28541 Submitted by: dbader@eece.unm.edu 2001-07-04 10:39:40 +02:00			`SUBDIR += grappa`
Turn on hmmer. 1998-07-13 01:30:50 +02:00			`SUBDIR += hmmer`
Jalview is a multiple alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) and is also available as a general purpose alignment editor. WWW: http://www.jalview.org PR: 93054 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> 2006-02-13 10:42:13 +01:00			`SUBDIR += jalview`
Activate kinemage 1998-01-29 18:25:59 +01:00			`SUBDIR += kinemage`
Add lagan 1.2, efficient tools for large-scale multiple alignments of genomic DNA. PR: ports/93058 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> 2006-03-16 23:31:26 +01:00			`SUBDIR += lagan`
Add lamarc 2001.08.06, a package of programs for computing population parameters. 2001-08-07 10:17:58 +02:00			`SUBDIR += lamarc`
add libgenome 0.5.0 Toolkit for developing bioinformatic related software in C++ 2002-07-30 12:57:06 +02:00			`SUBDIR += libgenome`
Folding@Home is a distributed computing project -- people from through out the world download and run software to band together to make one of the largest supercomputers in the world. Every computer makes the project closer to our goals. Folding@Home uses novel computational methods coupled to distributed computing, to simulate problems thousands to millions of times more challenging than previously achieved. WWW: http://folding.standford.edu PR: ports/101235 Submitted by: Yonatan <onatan@gmail.com> 2006-08-29 00:33:45 +02:00			`SUBDIR += linux-foldingathome`
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> 2003-09-03 04:23:23 +02:00			`SUBDIR += lsysexp`
Add mafft 5.734, multiple sequence alignments based on fast Fourier transform. PR: ports/93059 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> 2006-03-15 11:41:16 +01:00			`SUBDIR += mafft`
Add migrate 1.2, a program to estimate population sizes and migration rates. 2001-08-06 15:07:46 +02:00			`SUBDIR += migrate`
Add platon and molden 1999-05-07 08:59:25 +02:00			`SUBDIR += molden`
Add mopac and psi88 (Move mopac and psi88 from misc to biology) 1999-05-06 10:18:35 +02:00			`SUBDIR += mopac`
MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. WWW: http://mrbayes.csit.fsu.edu/ PR: ports/118542 Submitted by: mzaki at biol.s.u-tokyo.ac.jp 2007-12-15 16:13:41 +01:00			`SUBDIR += mrbayes`
MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. WWW: http://mummer.sourceforge.net/ PR: ports/118142 Submitted by: Tony Maher 2007-12-14 21:54:47 +01:00			`SUBDIR += mummer`
This is nab (nucleic acid builder), a language for macromolecules PR: 21585 Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU> 2000-10-10 04:56:57 +02:00			`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 14:56:24 +01:00			`SUBDIR += ncbi-toolkit`
Added deft and ortep3 1999-05-19 15:38:46 +02:00			`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 15:16:10 +02:00			`SUBDIR += p5-AcePerl`
Add p5-Bio-ASN1-EntrezGene, a Regular expression-based Perl Parser for NCBI Entrez Gene. PR: 87423 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> Approved by: novel (mentor) (implicit) 2005-10-15 22:09:50 +02:00			`SUBDIR += p5-Bio-ASN1-EntrezGene`
Add p5-Bio-Das 1.02, client-side library for Distributed Genome Annotation System. PR: ports/76379 Submitted by: Razi Khaja <razi@genet.sickkids.on.ca> 2005-09-01 15:09:32 +02:00			`SUBDIR += p5-Bio-Das`
Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl. Approved by: tobez (implicit) 2006-05-13 18:48:15 +02:00			`SUBDIR += p5-Bio-Phylo`
Add BioPerl, a collection of Perl5 mods for bioinformatics/genomics PR: ports/20252 Submitted by: Johann Visagie <johann@egenetics.com> 2000-07-28 16:06:03 +02:00			`SUBDIR += p5-bioperl`
- Re-add p5-bioperl-devel, development version of biology/p5-bioperl (A collection of Perl modules for bioinformatics) PR: ports/89497 Submitted by: Mauricio Herrera Cuadra <arareko@yahoo.com> 2005-12-02 22:40:12 +01:00			`SUBDIR += p5-bioperl-devel`
Bioperl-run contain modules that provides a PERL interface to various bioinformatics applications. This allows various applications to be used with common Bioperl objects. WWW: http://bioperl.org/ PR: ports/93674 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> 2006-05-02 23:30:08 +02:00			`SUBDIR += p5-bioperl-run`
Bioperl-run contain modules that provides a PERL interface to various bioinformatics applications. This allows various applications to be used with common Bioperl objects. WWW: http://bioperl.org/ PR: ports/93675 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> 2006-05-02 23:31:43 +02:00			`SUBDIR += p5-bioperl-run-devel`
Activating the chemeq, clustalw, paml, and phylip ports. 2000-07-10 05:26:57 +02:00			`SUBDIR += paml`
			`SUBDIR += phylip`
Add platon and molden 1999-05-07 08:59:25 +02:00			`SUBDIR += platon`
Activate povchem. 1998-03-16 08:01:32 +01:00			`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 17:31:09 +02:00			`SUBDIR += primer3`
Add protomol 2.0.3, OO, component based, framework for molecular dynamics (MD) simulations. PR: 95123 Submitted by: Sangwoo Shim <sangwoos@gmail.com> 2006-05-05 22:09:54 +02:00			`SUBDIR += protomol`
Add mopac and psi88 (Move mopac and psi88 from misc to biology) 1999-05-06 10:18:35 +02:00			`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 14:12:24 +02:00			`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 13:53:43 +02:00			`SUBDIR += pymol`
Activate rasmol. 1997-12-15 18:47:41 +01:00			`SUBDIR += rasmol`
Add recombine 1.40, a program to fit population models across sites. 2001-08-06 16:49:53 +02:00			`SUBDIR += recombine`
Add ruby-bio (BioRuby), an integrated environment for Bioinformatics written in Ruby. 2001-10-24 08:21:52 +02:00			`SUBDIR += ruby-bio`
Activate seaview. 1997-12-21 23:05:43 +01:00			`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 14:07:26 +02:00			`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 16:33:00 +02:00			`SUBDIR += sim4`
Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection. PR: 33853 Submitted by: chuynh@biolateral.com.au 2002-03-27 15:18:49 +01:00			`SUBDIR += tRNAscan-SE`
Add t_coffee 1.37, a multiple DNA or protein sequence alignment package. 2002-01-25 15:58:16 +01:00			`SUBDIR += t_coffee`
Activate tinker. 1998-11-17 05:54:28 +01:00			`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 09:54:10 +01:00			`SUBDIR += treepuzzle`
Add treeviewx 0.1.1, a phylogenetic tree viewer. PR: 29770 Submitted by: Tony Maher <tonym@biolateral.com.au> 2001-08-17 10:39:28 +02:00			`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 15:58:40 +02:00			`SUBDIR += wise`
Add xdrawchem 0.82 - a program for drawing molecules 2000-07-19 15:23:02 +02:00			`SUBDIR += xdrawchem`
Added gperiodic and xmolwt 1999-09-06 22:09:12 +02:00			`SUBDIR += xmolwt`
The new ports category "biology" starts here today. No Darwin jokes please! 1997-12-13 06:54:24 +01:00
			`.include <bsd.port.subdir.mk>`