freebsd-ports/biology/Makefile

# $FreeBSD$
#

    COMMENT = Biology

    SUBDIR += L-Breeder
    SUBDIR += ariadne
    SUBDIR += artemis
    SUBDIR += avida
    SUBDIR += babel
    SUBDIR += belvu
    SUBDIR += biojava
    SUBDIR += blast
    SUBDIR += boinc-simap
    SUBDIR += clustalw
    SUBDIR += coalesce
    SUBDIR += blat
    SUBDIR += chemeq
    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 += gperiodic
    SUBDIR += grappa
    SUBDIR += hmmer
    SUBDIR += jalview
    SUBDIR += kinemage
    SUBDIR += lagan
    SUBDIR += lamarc
    SUBDIR += libgenome
    SUBDIR += lsysexp
    SUBDIR += mafft
    SUBDIR += migrate
    SUBDIR += molden
    SUBDIR += mopac
    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 04:58:03 +00:00			`# $FreeBSD$`
The new ports category "biology" starts here today. No Darwin jokes please! 1997-12-13 05:54:24 +00:00			`#`

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 07:29:48 +00:00			`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 00:01:59 +00:00			`SUBDIR += L-Breeder`
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 14:29:59 +00:00			`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 14:39:40 +00:00			`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 15:17:46 +00:00			`SUBDIR += avida`
Activate babel. 1997-12-21 21:58:57 +00:00			`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 10:24:57 +00:00			`SUBDIR += belvu`
Initial import of biology/biojava PR: 21678 Submitted by: Brad Chapman <chapmanb@arches.uga.edu> 2000-10-10 11:14:03 +00:00			`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 21:35:04 +00:00			`SUBDIR += blast`
SIMAP (Similarity Matrix of Proteins) is a public database of pre-calculated protein similarities that plays a key role in many bioinformatics methods. It contains about all currently published protein sequences and is continuously updated. The computational effort for keeping SIMAP up-to-date is constantly increasing. Please help to update SIMAP by calculating protein similarities on your computer. WWW: http://boinc.bio.wzw.tum.de/boincsimap/ 2006-06-19 20:32:08 +00:00			`SUBDIR += boinc-simap`
Activating the chemeq, clustalw, paml, and phylip ports. 2000-07-10 03:26:57 +00:00			`SUBDIR += clustalw`
Add coalesce 1.50, a program to fit population models. 2001-08-06 14:41:58 +00:00			`SUBDIR += coalesce`
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 10:26:12 +00:00			`SUBDIR += blat`
- 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 19:47:59 +00:00			`SUBDIR += chemeq`
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 14:42:56 +00:00			`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 03:07:59 +00:00			`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 03:20:48 +00:00			`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 10:35:24 +00:00			`SUBDIR += dotter`
[new port] biology/embassy PR: ports/74330 Submitted by: Fernan Aguero <fernan(at)iib.unsam.edu.ar> 2004-11-26 16:34:22 +00:00			`SUBDIR += embassy`
Add emboss, the European Molecular Biology Open Software Suite PR: ports/20317 Submitted by: Johann Visagie <johann@egenetics.com> 2000-07-31 19:13:54 +00:00			`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 16:24:18 +00:00			`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 16:28:59 +00:00			`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 12:31:13 +00:00			`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 21:16:16 +00:00			`SUBDIR += finchtv`
Add fluctuate 1.30, a program to fit population models. 2001-08-06 14:45:39 +00:00			`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 06:38:37 +00:00			`SUBDIR += garlic`
reimport biology/genpak 2001-02-28 02:46:51 +00:00			`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 10:03:26 +00:00			`SUBDIR += gff2ps`
Added gperiodic and xmolwt 1999-09-06 20:09:12 +00:00			`SUBDIR += gperiodic`
Add grappa 1.0.2, Genome Rearrangements Analysis and Phylogeny Software. PR: 28541 Submitted by: dbader@eece.unm.edu 2001-07-04 08:39:40 +00:00			`SUBDIR += grappa`
Turn on hmmer. 1998-07-12 23:30:50 +00:00			`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 09:42:13 +00:00			`SUBDIR += jalview`
Activate kinemage 1998-01-29 17:25:59 +00:00			`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 22:31:26 +00:00			`SUBDIR += lagan`
Add lamarc 2001.08.06, a package of programs for computing population parameters. 2001-08-07 08:17:58 +00:00			`SUBDIR += lamarc`
add libgenome 0.5.0 Toolkit for developing bioinformatic related software in C++ 2002-07-30 10:57:06 +00:00			`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> 2003-09-03 02:23:23 +00:00			`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 10:41:16 +00:00			`SUBDIR += mafft`
Add migrate 1.2, a program to estimate population sizes and migration rates. 2001-08-06 13:07:46 +00:00			`SUBDIR += migrate`
Add platon and molden 1999-05-07 06:59:25 +00:00			`SUBDIR += molden`
Add mopac and psi88 (Move mopac and psi88 from misc to biology) 1999-05-06 08:18:35 +00:00			`SUBDIR += mopac`
This is nab (nucleic acid builder), a language for macromolecules PR: 21585 Submitted by: M. L. Dodson <bdodson@scms.utmb.EDU> 2000-10-10 02:56:57 +00:00			`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 13:56:24 +00:00			`SUBDIR += ncbi-toolkit`
Added deft and ortep3 1999-05-19 13:38:46 +00:00			`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 13:16:10 +00:00			`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 20:09:50 +00:00			`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 13:09:32 +00:00			`SUBDIR += p5-Bio-Das`
Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl. Approved by: tobez (implicit) 2006-05-13 16:48:15 +00:00			`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 14:06:03 +00:00			`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 21:40:12 +00:00			`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 21:30:08 +00:00			`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 21:31:43 +00:00			`SUBDIR += p5-bioperl-run-devel`
Activating the chemeq, clustalw, paml, and phylip ports. 2000-07-10 03:26:57 +00:00			`SUBDIR += paml`
			`SUBDIR += phylip`
Add platon and molden 1999-05-07 06:59:25 +00:00			`SUBDIR += platon`
Activate povchem. 1998-03-16 07:01:32 +00:00			`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 15:31:09 +00:00			`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 20:09:54 +00:00			`SUBDIR += protomol`
Add mopac and psi88 (Move mopac and psi88 from misc to biology) 1999-05-06 08:18:35 +00:00			`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 12:12:24 +00:00			`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 11:53:43 +00:00			`SUBDIR += pymol`
Activate rasmol. 1997-12-15 17:47:41 +00:00			`SUBDIR += rasmol`
Add recombine 1.40, a program to fit population models across sites. 2001-08-06 14:49:53 +00:00			`SUBDIR += recombine`
Add ruby-bio (BioRuby), an integrated environment for Bioinformatics written in Ruby. 2001-10-24 06:21:52 +00:00			`SUBDIR += ruby-bio`
Activate seaview. 1997-12-21 22:05:43 +00:00			`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 12:07:26 +00:00			`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 14:33:00 +00:00			`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 14:18:49 +00:00			`SUBDIR += tRNAscan-SE`
Add t_coffee 1.37, a multiple DNA or protein sequence alignment package. 2002-01-25 14:58:16 +00:00			`SUBDIR += t_coffee`
Activate tinker. 1998-11-17 04:54:28 +00:00			`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 08:54:10 +00:00			`SUBDIR += treepuzzle`
Add treeviewx 0.1.1, a phylogenetic tree viewer. PR: 29770 Submitted by: Tony Maher <tonym@biolateral.com.au> 2001-08-17 08:39:28 +00:00			`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 13:58:40 +00:00			`SUBDIR += wise`
Add xdrawchem 0.82 - a program for drawing molecules 2000-07-19 13:23:02 +00:00			`SUBDIR += xdrawchem`
Added gperiodic and xmolwt 1999-09-06 20:09:12 +00:00			`SUBDIR += xmolwt`
The new ports category "biology" starts here today. No Darwin jokes please! 1997-12-13 05:54:24 +00:00
			`.include <bsd.port.subdir.mk>`