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* Teach the building cluster that these ports are not to be buildEdwin Groothuis2008-05-254-0/+12
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* New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis2008-05-249-0/+221
| | | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis2008-05-244-0/+22
| | | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis2008-05-242-0/+49
| | | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis2008-05-249-0/+1174
| | | | | | | | | | | | | | | | | | | | | | | | | | assembly Consed is a tool for viewing, editing, and finishing sequence assemblies. The port is constituted of 4 parts: biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing biology/consed: workbench biology/phd2fasta: small utility All these can be used separately; however, most function of consed depends on the others. Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to get the softwares. Phred (including phd2fasta) and phrap are emailed, and consed can be downloaded to a restricted IP address. For commercial users, the licensing fee is ca. $10,000 at the time of writing. PR: ports/118548 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* Update to 1.08Mathieu Arnold2008-05-232-4/+4
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* - Update MASTER_SITES and WWW: lineMartin Wilke2008-05-224-61/+46
| | | | | | | | - Support CC/CFLAGS properly - Strip binary PR: 123866 Submitted by: Ports Fury
* - Include some ports in perl5 category.Marcelo Araujo2008-05-191-1/+1
| | | | | | | PR: ports/123530 Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com> Reworked by: araujo (myself) Approved by: flz (portmgr)
* - Update maintainer's email addressPav Lucistnik2008-05-173-3/+3
| | | | Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
* - Try to fix fetchPav Lucistnik2008-05-171-0/+2
| | | | Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
* Update to 1.23Erwin Lansing2008-05-152-4/+4
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* NJplot is a tree drawing program able to draw any phylogenetic tree expressedPav Lucistnik2008-05-145-0/+145
| | | | | | | | | | | | | | | | | | | | | | in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. The package contains the following programs: njplot - draw phylogenetic trees and interactively modify them newicktops - non-interactive version rendering into a PostScript file newicktotxt - non-interactive version rendering into a text file unrooted - draw unrooted circular trees If you use NJplot in a published work, please cite the following reference: Perriere, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system for biological sequence banks. Biochimie, 78, 364-369. WWW: http://pbil.univ-lyon1.fr/software/njplot.html PR: ports/118438 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* MUSCLE is multiple alignment software for protein and nucleotide sequences.Pav Lucistnik2008-05-147-0/+232
| | | | | | | | | | | | | | | | | | | | | | | | | | | The name stands for multiple sequence comparison by log-expectation. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that give the best average accuracy in the published tests. MUSCLE can achieve both better average accuracy and better speed than CLUSTALW or T-Coffee, depending on the chosen options. Citation: Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792-1797. Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(1): 113. The NAR paper gives only a brief overview of the algorithm and implementation details. For a full discussion of the method and many of the non-default options that it offers, please see the BMC paper. WWW: http://www.drive5.com/muscle/ PR: ports/118460 Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* - add PORTSCOUTDirk Meyer2008-05-041-0/+2
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* Update to version 34.OKAZAKI Tetsurou2008-04-302-11/+5
| | | | | | | Remove BROKEN. PR: 123218 Submitted by: maintainer
* - update to 0.8.2Dirk Meyer2008-04-299-456/+205
| | | | | - take maintainership Approved by: maintainer
* - Update to 2.0.6Martin Wilke2008-04-292-5/+5
| | | | | | | - Pass maintainership to submitter PR: 123193 Submitted by: Wen heping <wenheping@gmail.com>
* Reset aaron's port maintainerships due to many maintainer-timeouts.Mark Linimon2008-04-291-1/+1
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* - Mark BROKEN on -CURRENT: error: 'linkat' redeclared as different kind of ↵Pav Lucistnik2008-04-251-0/+4
| | | | | | symbol Reported by: pointyhat
* - Remove unneeded dependency from gtk12/gtk20 [1]Martin Wilke2008-04-1919-50/+43
| | | | | | | | | | | | | | | - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG - Remove X11BASE support in favor of LOCALBASE or PREFIX - Use USE_LDCONFIG instead of INSTALLS_SHLIB - Remove unneeded USE_GCC 3.4+ Thanks to all Helpers: Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr, ehaupt, nox, itetcu, flz, pav PR: 116263 Tested on: pointyhat Approved by: portmgr (pav)
* implement @dirrmtry macro for the pkg-plistEdwin Groothuis2008-04-191-1/+1
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* - Update mastersite.Jean Milanez Melo2008-04-181-1/+2
| | | | | PR: ports/122130 Submitted by: Ganael Laplanche <ganael.laplanche@martymac.com>
* - Replace SF with second working master sitePav Lucistnik2008-04-171-1/+1
| | | | Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Take advantage of CPAN macro from bsd.sites.mk, change ↵Marcelo Araujo2008-04-176-10/+6
| | | | | | | | | ${MASTER_SITE_PERL_CPAN} to CPAN. PR: ports/122674 Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com> Reworked by: araujo (myself) Approved by: portmgr (pav)
* - It seems that upstream removes their distfiles from sourceforge, so addRong-En Fan2008-04-171-1/+2
| | | | | | the download site pointed by their webpage as first choice. Noticed by: pointyhat via pav
* - Update to 5.0.0Rong-En Fan2008-04-1317-6851/+707
| | | | | PR: ports/122437 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
* - Sort pkg-plist before updating to 5.0.0Rong-En Fan2008-04-131-888/+888
| | | | | PR: ports/122437 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* Change maintainers e-mail address.Emanuel Haupt2008-04-101-2/+2
| | | | Requested over: IRC
* - Update to 35.3.6Cheng-Lung Sung2008-04-102-5/+5
| | | | | PR: ports/122607 Submitted by: maintainer (Fernan Aguero)
* - Chase the gsl shared lib bump.Philippe Audeoud2008-04-081-2/+2
| | | | Approved by: thierry (mentor)
* - Update maintainer's emailRong-En Fan2008-04-061-3/+5
| | | | | | | - Mark as deprecated PR: ports/122474 Submitted by: M. L. Dodson <mldodson at comcast.net> (maintainer with another email)
* MAPMAKER/EXP is a linkage analysis package designed to help construct primaryRong-En Fan2008-04-0628-0/+1101
| | | | | | | | | | | | | | | | | | linkage maps of markers segregating in experimental crosses. MAPMAKER/EXP performs full multipoint linkage analysis (simultaneous estimation of all recombination fractions from the primary data) for dominant, recessive, and co- dominant (e.g. RFLP-like) markers. MAPMAKER/EXP is an experimental-cross-only successor to the original MAPMAKER program. MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map genes controlling polygenic quantitative traits in F2 intercrosses and BC1 backcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL can be found in the technical report (included with MAPMAKER/QTL). WWW: http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/ PR: ports/122452 Submitted by: Tassilo Philipp <tphilipp at potion-studios.com>
* - Update to 5.68Rong-En Fan2008-04-053-10/+10
| | | | | | | - Remove gcc version restriction PR: ports/122435 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer)
* - Update to 1.1.3Pav Lucistnik2008-04-043-185/+203
| | | | | | PR: ports/122374 Submitted by: Wen heping <wenheping@gmail.com> Patch revised: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
* - Chase fasta3 updatePav Lucistnik2008-04-011-1/+1
| | | | Reported by: pointyhat
* - Update to 35.3.5Rong-En Fan2008-03-303-53/+49
| | | | | | | | | | - Switch to .tar.gz distfile so that we don't define our do-extract - While I'm here, using substitution for version numbers in pkg-plist for easier upgrade PR: ports/121690 Submitted by: Wen heping <wenheping at gmail.com> Approved by: maintainer timeout (2 weeks)
* - Fix build with GCC 4.2Pietro Cerutti2008-03-282-5/+18
| | | | Approved by: miwi (mentor)
* - Add missing dependensMartin Wilke2008-03-271-1/+3
| | | | | | - Bump PORTREVISION Submitted by: pointyhat via pav
* - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORGMartin Wilke2008-03-251-2/+1
| | | | | | - Bump PORTREVISION Approved by: portmgr (xorg cleanup)
* - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORGMartin Wilke2008-03-241-2/+2
| | | | | | - Bump PORTREVISION Approved by: portmgr (xorg cleanup)
* - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORGMartin Wilke2008-03-231-2/+1
| | | | | | - Bump PORTREVISION Approved by: portmgr (xorg cleanup)
* - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORGMartin Wilke2008-03-233-6/+3
| | | | | | - Bump PORTREVISION Approved by: portmgr (xorg cleanup)
* - Remove USE_X_PREFIXBeech Rintoul2008-03-212-4/+2
| | | | | | - Bump portrevision Approved by: David Yeske <dyeske@gmail.com> (maintainer, implicit)
* - Update to 2.0.5Philippe Audeoud2008-03-191-5/+10
| | | | | | | | - Add RESTRICTED due to non-commercial use licence. PR: ports/121794 Submitted by: KATO Tsuguru <tkato432@yahoo.com> Approved by: thierry and tabthorpe (mentors)
* - Update to version 2.0.5Philippe Audeoud2008-03-192-21/+10
| | | | | | | | - Add RESTRICTED due to a non-commercial use licence. PR: ports/121794 Submitted by: KATO Tsuguru <tkato432@yahoo.com> Approved by: thierry and tabthorpe (mentors)
* - Update to 1.07Martin Wilke2008-03-122-4/+4
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* Fix pkg-plistMaho Nakata2008-03-101-0/+142
| | | | Submitted by: pav
* Update to 1.0r2.Maho Nakata2008-03-076-955/+636
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* - File was rerolled for a small bugfix.Martin Wilke2008-02-273-3/+16
| | | | Submitted by: pointyhat via pav/erwin
* - Restore clustalw symlink, other ports rely on itPav Lucistnik2008-02-261-1/+5
| | | | | Reported by: pointyhat Pointy hat to: pav
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