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2008-05-31- Update to 1.09Martin Wilke2-4/+4
Notes: svn path=/head/; revision=214021
2008-05-25Teach the building cluster that these ports are not to be buildEdwin Groothuis4-0/+12
Notes: svn path=/head/; revision=213667
2008-05-24New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis9-0/+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> Notes: svn path=/head/; revision=213596
2008-05-24New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis4-0/+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> Notes: svn path=/head/; revision=213594
2008-05-24New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis2-0/+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> Notes: svn path=/head/; revision=213592
2008-05-24New port: biology/consed viewing and editing workbench for sequenceEdwin Groothuis9-0/+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> Notes: svn path=/head/; revision=213590
2008-05-23Update to 1.08Mathieu Arnold2-4/+4
Notes: svn path=/head/; revision=213548
2008-05-22- Update MASTER_SITES and WWW: lineMartin Wilke4-61/+46
- Support CC/CFLAGS properly - Strip binary PR: 123866 Submitted by: Ports Fury Notes: svn path=/head/; revision=213507
2008-05-19- Include some ports in perl5 category.Marcelo Araujo1-1/+1
PR: ports/123530 Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com> Reworked by: araujo (myself) Approved by: flz (portmgr) Notes: svn path=/head/; revision=213332
2008-05-17- Update maintainer's email addressPav Lucistnik3-3/+3
Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer) Notes: svn path=/head/; revision=213206
2008-05-17- Try to fix fetchPav Lucistnik1-0/+2
Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer) Notes: svn path=/head/; revision=213205
2008-05-15Update to 1.23Erwin Lansing2-4/+4
Notes: svn path=/head/; revision=213074
2008-05-14NJplot is a tree drawing program able to draw any phylogenetic tree expressedPav Lucistnik5-0/+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> Notes: svn path=/head/; revision=213034
2008-05-14MUSCLE is multiple alignment software for protein and nucleotide sequences.Pav Lucistnik7-0/+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> Notes: svn path=/head/; revision=213031
2008-05-04- add PORTSCOUTDirk Meyer1-0/+2
Notes: svn path=/head/; revision=212589
2008-04-30Update to version 34.OKAZAKI Tetsurou2-11/+5
Remove BROKEN. PR: 123218 Submitted by: maintainer Notes: svn path=/head/; revision=212384
2008-04-29- update to 0.8.2Dirk Meyer9-456/+205
- take maintainership Approved by: maintainer Notes: svn path=/head/; revision=212268
2008-04-29- Update to 2.0.6Martin Wilke2-5/+5
- Pass maintainership to submitter PR: 123193 Submitted by: Wen heping <wenheping@gmail.com> Notes: svn path=/head/; revision=212249
2008-04-29Reset aaron's port maintainerships due to many maintainer-timeouts.Mark Linimon1-1/+1
Notes: svn path=/head/; revision=212202
2008-04-25- Mark BROKEN on -CURRENT: error: 'linkat' redeclared as different kind of ↵Pav Lucistnik1-0/+4
symbol Reported by: pointyhat Notes: svn path=/head/; revision=211989
2008-04-19- Remove unneeded dependency from gtk12/gtk20 [1]Martin Wilke19-50/+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) Notes: svn path=/head/; revision=211584
2008-04-19implement @dirrmtry macro for the pkg-plistEdwin Groothuis1-1/+1
Notes: svn path=/head/; revision=211557
2008-04-18- Update mastersite.Jean Milanez Melo1-1/+2
PR: ports/122130 Submitted by: Ganael Laplanche <ganael.laplanche@martymac.com> Notes: svn path=/head/; revision=211533
2008-04-17- Replace SF with second working master sitePav Lucistnik1-1/+1
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=211457
2008-04-17- Take advantage of CPAN macro from bsd.sites.mk, change ↵Marcelo Araujo6-10/+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) Notes: svn path=/head/; revision=211450
2008-04-17- It seems that upstream removes their distfiles from sourceforge, so addRong-En Fan1-1/+2
the download site pointed by their webpage as first choice. Noticed by: pointyhat via pav Notes: svn path=/head/; revision=211422
2008-04-13- Update to 5.0.0Rong-En Fan17-6851/+707
PR: ports/122437 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=211152
2008-04-13- Sort pkg-plist before updating to 5.0.0Rong-En Fan1-888/+888
PR: ports/122437 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=211151
2008-04-10Change maintainers e-mail address.Emanuel Haupt1-2/+2
Requested over: IRC Notes: svn path=/head/; revision=211013
2008-04-10- Update to 35.3.6Cheng-Lung Sung2-5/+5
PR: ports/122607 Submitted by: maintainer (Fernan Aguero) Notes: svn path=/head/; revision=210980
2008-04-08- Chase the gsl shared lib bump.Philippe Audeoud1-2/+2
Approved by: thierry (mentor) Notes: svn path=/head/; revision=210850
2008-04-06- Update maintainer's emailRong-En Fan1-3/+5
- Mark as deprecated PR: ports/122474 Submitted by: M. L. Dodson <mldodson at comcast.net> (maintainer with another email) Notes: svn path=/head/; revision=210633
2008-04-06MAPMAKER/EXP is a linkage analysis package designed to help construct primaryRong-En Fan28-0/+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> Notes: svn path=/head/; revision=210625
2008-04-05- Update to 5.68Rong-En Fan3-10/+10
- Remove gcc version restriction PR: ports/122435 Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=210568
2008-04-04- Update to 1.1.3Pav Lucistnik3-185/+203
PR: ports/122374 Submitted by: Wen heping <wenheping@gmail.com> Patch revised: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=210539
2008-04-01- Chase fasta3 updatePav Lucistnik1-1/+1
Reported by: pointyhat Notes: svn path=/head/; revision=210344
2008-03-30- Update to 35.3.5Rong-En Fan3-53/+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) Notes: svn path=/head/; revision=210155
2008-03-28- Fix build with GCC 4.2Pietro Cerutti2-5/+18
Approved by: miwi (mentor) Notes: svn path=/head/; revision=210034
2008-03-27- Add missing dependensMartin Wilke1-1/+3
- Bump PORTREVISION Submitted by: pointyhat via pav Notes: svn path=/head/; revision=209943
2008-03-25- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORGMartin Wilke1-2/+1
- Bump PORTREVISION Approved by: portmgr (xorg cleanup) Notes: svn path=/head/; revision=209811
2008-03-24- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORGMartin Wilke1-2/+2
- Bump PORTREVISION Approved by: portmgr (xorg cleanup) Notes: svn path=/head/; revision=209683
2008-03-23- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORGMartin Wilke1-2/+1
- Bump PORTREVISION Approved by: portmgr (xorg cleanup) Notes: svn path=/head/; revision=209644
2008-03-23- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORGMartin Wilke3-6/+3
- Bump PORTREVISION Approved by: portmgr (xorg cleanup) Notes: svn path=/head/; revision=209636
2008-03-21- Remove USE_X_PREFIXBeech Rintoul2-4/+2
- Bump portrevision Approved by: David Yeske <dyeske@gmail.com> (maintainer, implicit) Notes: svn path=/head/; revision=209552
2008-03-19- Update to 2.0.5Philippe Audeoud1-5/+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) Notes: svn path=/head/; revision=209377
2008-03-19- Update to version 2.0.5Philippe Audeoud2-21/+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) Notes: svn path=/head/; revision=209372
2008-03-12- Update to 1.07Martin Wilke2-4/+4
Notes: svn path=/head/; revision=208888
2008-03-10Fix pkg-plistMaho Nakata1-0/+142
Submitted by: pav Notes: svn path=/head/; revision=208704
2008-03-07Update to 1.0r2.Maho Nakata6-955/+636
Notes: svn path=/head/; revision=208552
2008-02-27- File was rerolled for a small bugfix.Martin Wilke3-3/+16
Submitted by: pointyhat via pav/erwin Notes: svn path=/head/; revision=207980
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