aboutsummaryrefslogtreecommitdiff
path: root/biology
Commit message (Collapse)AuthorAgeFilesLines
* Update CONFIGURE_ARGS for how we pass CONFIGURE_TARGET to configure script.Rong-En Fan2008-08-214-5/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Specifically, newer autoconf (> 2.13) has different semantic of the configure target. In short, one should use --build=CONFIGURE_TARGET instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning and the old semantic may be removed in later autoconf releases. To workaround this issue, many ports hack the CONFIGURE_TARGET variable so that it contains the ``--build='' prefix. To solve this issue, under the fact that some ports still have configure script generated by the old autoconf, we use runtime detection in the do-configure target so that the proper argument can be used. Changes to Mk/*: - Add runtime detection magic in bsd.port.mk - Remove CONFIGURE_TARGET hack in various bsd.*.mk - USE_GNOME=gnometarget is now an no-op Changes to individual ports, other than removing the CONFIGURE_TARGET hack: = pkg-plist changed (due to the ugly CONFIGURE_TARGET prefix in * executables) - comms/gnuradio - science/abinit - science/elmer-fem - science/elmer-matc - science/elmer-meshgen2d - science/elmerfront - science/elmerpost = use x86_64 as ARCH - devel/g-wrap = other changes - print/magicfilter GNU_CONFIGURE -> HAS_CONFIGURE since it's not generated by autoconf Total # of ports modified: 1,027 Total # of ports affected: ~7,000 (set GNU_CONFIGURE to yes) PR: 126524 (obsoletes 52917) Submitted by: rafan Tested on: two pointyhat 7-amd64 exp runs (by pav) Approved by: portmgr (pav) Notes: svn path=/head/; revision=218938
* Unbreak building for 8-x.Boris Samorodov2008-08-152-4/+114
| | | | | | | Submitted by: Steve Kargl <sgk at troutmask.apl.washington.edu> at ports@ ML Notes: svn path=/head/; revision=218644
* - update PORTSCOUTDirk Meyer2008-08-121-1/+3
| | | | Notes: svn path=/head/; revision=218469
* - Update to 1.47Martin Wilke2008-08-113-53/+92
| | | | | | | | | PR: 125912 Submitted by: Wen heping <wenheping@gmail.com> Approved by: maintainer timeout Notes: svn path=/head/; revision=218425
* - Update to 2.1.3Philip M. Gollucci2008-07-313-4/+5
| | | | | | | Approved by: gabor (mentor) Notes: svn path=/head/; revision=217884
* - Remove USE_GCC where it can be satisfied with base compiler on followingPav Lucistnik2008-07-252-2/+0
| | | | | | | FreeBSD versions: 5.3 and up, 6.x, 7.x, 8-CURRENT Notes: svn path=/head/; revision=217485
* - Remove duplicates from MAKE_ENV after inclusion of CC and CXX in default ↵Pav Lucistnik2008-07-253-3/+5
| | | | | | | MAKE_ENV Notes: svn path=/head/; revision=217468
* - Delete biology/nab port after being marked DEPRECATED for three monthsPav Lucistnik2008-07-2415-1093/+0
| | | | | | | | PR: ports/125891 Submitted by: M. L. Dodson <mldodson@comcast.net> (maintainer) Notes: svn path=/head/; revision=217415
* Update my ports to my freebsd addressPhilip M. Gollucci2008-07-232-2/+2
| | | | | | | Approved by: araujo (mentor) Notes: svn path=/head/; revision=217338
* - respect NOPORTEXAMPLES/NOPORTDOCS and fix plistIon-Mihai Tetcu2008-07-122-14/+15
| | | | | | | | | - bump PORTREVISION Prompted by: QA Tindy run Notes: svn path=/head/; revision=216729
* - Update to 2.1.2c.Marcelo Araujo2008-07-112-5/+5
| | | | | | | | | | - Pass maintainership to submitter. PR: ports/125497 Submitted by: Philip M. Gollucci <pgollucci@p6m7g8.com> Notes: svn path=/head/; revision=216706
* - extened PORTSCOUTDirk Meyer2008-07-081-1/+1
| | | | Notes: svn path=/head/; revision=216541
* - Mark BROKEN: missing cpan dependency (interactive loop)Pav Lucistnik2008-07-071-0/+2
| | | | Notes: svn path=/head/; revision=216502
* - Bump portrevision after openbabel updateBeech Rintoul2008-07-071-1/+1
| | | | Notes: svn path=/head/; revision=216430
* - Update to 1.5.2.Felippe de Meirelles Motta2008-07-064-1355/+1063
| | | | | | | | | | PR: ports/124648 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer) Reviewed by: lippe Approved by: gabor (mentor, implicit) Notes: svn path=/head/; revision=216421
* - Update to 1.45Beech Rintoul2008-07-043-26/+79
| | | | | | | | | PR: ports/125134 Submitted by: Wen heping <wenheping@gmail.com> Approved by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer) Notes: svn path=/head/; revision=216283
* - extend PORTSCOUTDirk Meyer2008-06-241-1/+1
| | | | Notes: svn path=/head/; revision=215701
* - Fix plist files installation.Felippe de Meirelles Motta2008-06-211-1/+2
| | | | | | | | | | - Bump PORTREVISION. Reported by: QA Tindy Approved by: gabor (mentor, implicit) Notes: svn path=/head/; revision=215432
* SSAHA is a software tool for very fast matching and alignment of DNAFelippe de Meirelles Motta2008-06-2136-0/+1362
| | | | | | | | | | | | | | | | sequences. It stands for Sequence Search and Alignment by Hashing Algorithm. It achieves its fast search speed by converting sequence information into a `hash table' data structure, which can then be searched very rapidly for matches. WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/ PR: ports/124525 Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> Approved by: gabor (mentor, implicit) Notes: svn path=/head/; revision=215429
* - Fix fetch, update WWWPav Lucistnik2008-06-182-2/+2
| | | | Notes: svn path=/head/; revision=215107
* - Fix build dependsPietro Cerutti2008-06-091-0/+3
| | | | | | | | | - Bump port revision Reported by: pointyhat via pav Notes: svn path=/head/; revision=214547
* Bump portrevision due to upgrade of devel/gettext.Edwin Groothuis2008-06-0613-11/+13
| | | | | | | | | | | | | The affected ports are the ones with gettext as a run-dependency according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT in Makefile (29 of them). PR: ports/124340 Submitted by: edwin@ Approved by: portmgr (pav) Notes: svn path=/head/; revision=214428
* - Update to 3.67Pietro Cerutti2008-06-032-12/+7
| | | | | | | - Sanitize Makefile a little bit Notes: svn path=/head/; revision=214280
* - cleanup FreeBSD 5.xDirk Meyer2008-06-011-7/+1
| | | | Notes: svn path=/head/; revision=214138
* - Update to 1.09Martin Wilke2008-05-312-4/+4
| | | | Notes: svn path=/head/; revision=214021
* Teach the building cluster that these ports are not to be buildEdwin Groothuis2008-05-254-0/+12
| | | | Notes: svn path=/head/; revision=213667
* 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> Notes: svn path=/head/; revision=213596
* 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> Notes: svn path=/head/; revision=213594
* 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> Notes: svn path=/head/; revision=213592
* 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> Notes: svn path=/head/; revision=213590
* Update to 1.08Mathieu Arnold2008-05-232-4/+4
| | | | Notes: svn path=/head/; revision=213548
* - Update MASTER_SITES and WWW: lineMartin Wilke2008-05-224-61/+46
| | | | | | | | | | | - Support CC/CFLAGS properly - Strip binary PR: 123866 Submitted by: Ports Fury Notes: svn path=/head/; revision=213507
* - 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) Notes: svn path=/head/; revision=213332
* - Update maintainer's email addressPav Lucistnik2008-05-173-3/+3
| | | | | | | Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer) Notes: svn path=/head/; revision=213206
* - Try to fix fetchPav Lucistnik2008-05-171-0/+2
| | | | | | | Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer) Notes: svn path=/head/; revision=213205
* Update to 1.23Erwin Lansing2008-05-152-4/+4
| | | | Notes: svn path=/head/; revision=213074
* 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> Notes: svn path=/head/; revision=213034
* 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> Notes: svn path=/head/; revision=213031
* - add PORTSCOUTDirk Meyer2008-05-041-0/+2
| | | | Notes: svn path=/head/; revision=212589
* Update to version 34.OKAZAKI Tetsurou2008-04-302-11/+5
| | | | | | | | | | Remove BROKEN. PR: 123218 Submitted by: maintainer Notes: svn path=/head/; revision=212384
* - update to 0.8.2Dirk Meyer2008-04-299-456/+205
| | | | | | | | - take maintainership Approved by: maintainer Notes: svn path=/head/; revision=212268
* - Update to 2.0.6Martin Wilke2008-04-292-5/+5
| | | | | | | | | | - Pass maintainership to submitter PR: 123193 Submitted by: Wen heping <wenheping@gmail.com> Notes: svn path=/head/; revision=212249
* Reset aaron's port maintainerships due to many maintainer-timeouts.Mark Linimon2008-04-291-1/+1
| | | | Notes: svn path=/head/; revision=212202
* - Mark BROKEN on -CURRENT: error: 'linkat' redeclared as different kind of ↵Pav Lucistnik2008-04-251-0/+4
| | | | | | | | | symbol Reported by: pointyhat Notes: svn path=/head/; revision=211989
* - 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) Notes: svn path=/head/; revision=211584
* implement @dirrmtry macro for the pkg-plistEdwin Groothuis2008-04-191-1/+1
| | | | Notes: svn path=/head/; revision=211557
* - Update mastersite.Jean Milanez Melo2008-04-181-1/+2
| | | | | | | | PR: ports/122130 Submitted by: Ganael Laplanche <ganael.laplanche@martymac.com> Notes: svn path=/head/; revision=211533
* - Replace SF with second working master sitePav Lucistnik2008-04-171-1/+1
| | | | | | | Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) Notes: svn path=/head/; revision=211457
* - 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) Notes: svn path=/head/; revision=211450
* - 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 Notes: svn path=/head/; revision=211422
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-19 15:03:09 +0000