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Port details
fasta3 Collection of programs for searching DNA and protein databases
36.3.8 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
NO CDROM NO CDROM: May not be sold or incorporated into a commercial product
Maintainer: wendell@bsd.com.br search for ports maintained by this maintainer
Port Added: 11 Feb 2001 13:29:00
License: Fasta
Version 3 of the FASTA packages contains many programs for searching DNA and
protein databases and one program (prss3) for evaluating statistical
significance from randomly shuffled sequences.  Several additional analysis
programs, including programs that produce local alignments, are available as
part of version 2 of the FASTA package, which is available as the port
biology/fasta.

FASTA is described in:  W. R. Pearson and D. J. Lipman (1988), "Improved
Tools for Biological Sequence Analysis", PNAS 85:2444-2448; W. R.  Pearson
(1996) "Effective protein sequence comparison" Meth. Enzymol.  266:227-258;
Pearson et. al.  (1997) Genomics 46:24-36;  Pearson, (1999) Meth. in
Molecular Biology 132:185-219.

The FASTA3 suite is distributed freely subject to the condition that it may
not be sold or incorporated into a commercial product.

WWW: http://fasta.bioch.virginia.edu/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (128 items)
  1. /usr/local/share/licenses/fasta3-36.3.8/catalog.mk
  2. /usr/local/share/licenses/fasta3-36.3.8/LICENSE
  3. /usr/local/share/licenses/fasta3-36.3.8/Fasta
  4. bin/fasta36
  5. bin/fastf36
  6. bin/fastm36
  7. bin/fasts36
  8. bin/fastx36
  9. bin/fasty36
  10. bin/ggsearch36
  11. bin/glsearch36
  12. bin/lalign36
  13. bin/map_db
  14. bin/ssearch36
  15. bin/tfastf36
  16. bin/tfastm36
  17. bin/tfasts36
  18. bin/tfastx36
  19. bin/tfasty36
  20. etc/fastlibs.sample
  21. man/man1/fasta36.1.gz
  22. man/man1/fastf3.1.gz
  23. man/man1/fastf35.1.gz
  24. man/man1/fastm35.1.gz
  25. man/man1/fasts3.1.gz
  26. man/man1/fasts35.1.gz
  27. man/man1/fastx35.1.gz
  28. man/man1/fasty35.1.gz
  29. man/man1/ggsearch35.1.gz
  30. man/man1/lalign35.1.gz
  31. man/man1/map_db.1.gz
  32. man/man1/prfx35.1.gz
  33. man/man1/prss3.1.gz
  34. man/man1/prss35.1.gz
  35. man/man1/ps_lav.1.gz
  36. man/man1/ssearch35.1.gz
  37. man/man1/tfasta35.1.gz
  38. man/man1/tfastf35.1.gz
  39. man/man1/tfasts35.1.gz
  40. man/man1/tfastx35.1.gz
  41. man/man1/tfasty35.1.gz
  42. share/doc/fasta3/COPYRIGHT
  43. share/doc/fasta3/FASTA_LIST
  44. share/doc/fasta3/README
  45. share/doc/fasta3/README.versions
  46. share/doc/fasta3/changes_v34.html
  47. share/doc/fasta3/changes_v35.html
  48. share/doc/fasta3/changes_v36.html
  49. share/doc/fasta3/fasta.defaults
  50. share/doc/fasta3/fasta.options
  51. share/doc/fasta3/fasta_func.doc
  52. share/doc/fasta3/fasta_versions.html
  53. share/doc/fasta3/readme.v30
  54. share/doc/fasta3/readme.v30t6
  55. share/doc/fasta3/readme.v30t7
  56. share/doc/fasta3/readme.v31t0
  57. share/doc/fasta3/readme.v31t1
  58. share/doc/fasta3/readme.v32t0
  59. share/doc/fasta3/readme.v33t0
  60. share/doc/fasta3/readme.v34t0
  61. share/doc/fasta3/readme.v35
  62. share/doc/fasta3/readme.v36
  63. share/doc/fasta3/readme.w32
  64. share/examples/fasta3/bovgh.seq
  65. share/examples/fasta3/bovprl.seq
  66. share/examples/fasta3/dyr_human.aa
  67. share/examples/fasta3/egmsmg.aa
  68. share/examples/fasta3/gst.seq
  69. share/examples/fasta3/gstt1_drome.aa
  70. share/examples/fasta3/gtm1_human.aa
  71. share/examples/fasta3/gtt1_drome.aa
  72. share/examples/fasta3/h10_human.aa
  73. share/examples/fasta3/hahu.aa
  74. share/examples/fasta3/hsgstm1b.seq
  75. share/examples/fasta3/humgstd.seq
  76. share/examples/fasta3/lcbo.aa
  77. share/examples/fasta3/m1r.aa
  78. share/examples/fasta3/m2.aa
  79. share/examples/fasta3/mchu.aa
  80. share/examples/fasta3/mgstm1.aa
  81. share/examples/fasta3/mgstm1.lc
  82. share/examples/fasta3/mgstm1.seq
  83. share/examples/fasta3/mgstm1_genclone.seq
  84. share/examples/fasta3/mgtt2_x.seq
  85. share/examples/fasta3/ms1.aa
  86. share/examples/fasta3/mu.lib
  87. share/examples/fasta3/musplfm.aa
  88. share/examples/fasta3/mwkw.aa
  89. share/examples/fasta3/mwrtc1.aa
  90. share/examples/fasta3/myosin_bp.aa
  91. share/examples/fasta3/n0.aa
  92. share/examples/fasta3/n1.aa
  93. share/examples/fasta3/n2.aa
  94. share/examples/fasta3/n2_fs.lib
  95. share/examples/fasta3/n2s.aa
  96. share/examples/fasta3/n2t.aa
  97. share/examples/fasta3/n_fs.lib
  98. share/examples/fasta3/ngt.aa
  99. share/examples/fasta3/ngts.aa
  100. share/examples/fasta3/oohu.aa
  101. share/examples/fasta3/prio_atepa.aa
  102. share/examples/fasta3/prot_test.lib
  103. share/examples/fasta3/qrhuld.aa
  104. share/examples/fasta3/titin_hum.aa
  105. share/examples/fasta3/titin_hum.seq
  106. share/examples/fasta3/xurt8c.aa
  107. share/examples/fasta3/xurt8c.lc
  108. share/examples/fasta3/xurtg.aa
  109. share/fasta3/blosum45.mat
  110. share/fasta3/blosum50.mat
  111. share/fasta3/blosum62.mat
  112. share/fasta3/blosum80.mat
  113. share/fasta3/dna.mat
  114. share/fasta3/idn_aa.mat
  115. share/fasta3/md_10.mat
  116. share/fasta3/md_20.mat
  117. share/fasta3/md_40.mat
  118. share/fasta3/pam120.mat
  119. share/fasta3/pam250.mat
  120. share/fasta3/rna.mat
  121. share/fasta3/vtml160.mat
  122. share/fasta3/VTML_10.mat
  123. share/fasta3/VTML_120.mat
  124. share/fasta3/VTML_160.mat
  125. share/fasta3/VTML_20.mat
  126. share/fasta3/VTML_200.mat
  127. share/fasta3/VTML_40.mat
  128. share/fasta3/VTML_80.mat
  129. Collapse this list.

To install the port: cd /usr/ports/biology/fasta3/ && make install clean
To add the package: pkg install fasta3

PKGNAME: fasta3

distinfo:

SHA256 (fasta3/2014-01-29/fasta-36.3.8.tar.gz) = e235458afd16591bbcd5b89b639497e20346841091440a2445593318510a2262
SIZE (fasta3/2014-01-29/fasta-36.3.8.tar.gz) = 1211304

There are no ports dependent upon this port


Configuration Options
===> The following configuration options are available for fasta3-36.3.8:
     DOCS=on: Build and/or install documentation
     EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings

Master Sites:
  1. http://faculty.virginia.edu/wrpearson/fasta/fasta36/

Number of commits found: 45

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
19 May 2016 11:09:14
Original commit files touched by this commit  36.3.8
Revision:415503
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-messages

Approved by:	portmgr blanket
16 Oct 2015 13:31:10
Original commit files touched by this commit  36.3.8
Revision:399468
danilo search for other commits by this committer
- Update to 36.3.8
- Pass maintainership to submitter

PR:		203817
Submitted by:	Wendell Borges <wendell@bsd.com.br>
07 May 2015 02:33:58
Original commit files touched by this commit  36.3.7a
Revision:385592
wen search for other commits by this committer
- Update to 36.3.7a
20 Oct 2014 07:10:48
Original commit files touched by this commit  36.3.6d_1
Revision:371237
bapt search for other commits by this committer
Cleanup plist
02 Mar 2014 10:58:50
Original commit files touched by this commit  36.3.6d_1
Revision:346755
marino search for other commits by this committer
biology/fasta3: Checked new distfile and regenerated distinfo to unbreak

Fasta3 distfile was significantly changed.  This should have been released
as a new version (e.g. 36.3.6e), so it's not clear why the distfile was
rerolled.  There are significant changes to makefiles, conf files and even
a few .c and .h files.  They all look like legitimate updates to me
though.

Set DIST_SUBDIR since this port is now known for rerolling, then
regenerate distinfo.  Also add Fasta license and bump revision.
03 Jan 2014 19:46:05
Original commit files touched by this commit  36.3.6d
Revision:338577
bapt search for other commits by this committer
Mark as broken: Invalid checksum, seems like the software was rerolled
29 Oct 2013 19:32:16
Original commit files touched by this commit  36.3.6d
Revision:331982
pawel search for other commits by this committer
Update to version 36.3.6d

PR:		ports/181883
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
20 Sep 2013 15:55:44
Original commit files touched by this commit  36.3.6
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
07 Sep 2013 17:20:21
Original commit files touched by this commit  36.3.6
Revision:326658
sunpoet search for other commits by this committer
- Use single space after WWW:
19 Jul 2013 14:08:02
Original commit files touched by this commit  36.3.6
Revision:323293
wen search for other commits by this committer
- Update to 36.3.6
- Drop maintainership
01 Oct 2012 14:55:55
Original commit files touched by this commit  36.3.2
Revision:305131
wen search for other commits by this committer
- Take maintainership
01 Oct 2012 14:45:17
Original commit files touched by this commit  36.3.2
Revision:305130
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
22 Oct 2011 23:50:23
Original commit files touched by this commit  36.3.2
eadler search for other commits by this committer
- remove maintainer tags from pkg-descr

Approved by:    portmgr
Approved by:    bapt (mentor)
26 Jan 2011 20:26:36
Original commit files touched by this commit  36.3.2
beat search for other commits by this committer
- Update to 36.3.2 to fix distfile fetching on pointyhat

PR:             ports/154267
Submitted by:   Fernan Aguero <fernan AT iib.unsam.edu.ar> (maintainer)
Feature safe:   yes
23 Aug 2009 15:47:37
Original commit files touched by this commit  35.4.9
makc search for other commits by this committer
Update to 35.4.9

PR:             ports/137991
Submitted by:   Fernan Aguero (maintainer)
09 Jun 2009 07:53:37
Original commit files touched by this commit  35.4.7
itetcu search for other commits by this committer
- Update to 35.4.7 [1]
- Obey PREFIX [2]

Submitted by:   maintainer [1] [2]
Reported by:    QATty [2]
23 Feb 2009 16:13:19
Original commit files touched by this commit  35.4.4
amdmi3 search for other commits by this committer
- Add forgotten patch
23 Feb 2009 16:12:23
Original commit files touched by this commit  35.4.4
amdmi3 search for other commits by this committer
- Update to 35.4.4

PR:             132007
Submitted by:   Fernan Aguero <fernan at iib dot unsam dot edu dot ar>
(maintainer)
10 Apr 2008 08:09:10
Original commit files touched by this commit  35.3.6
clsung search for other commits by this committer
- Update to 35.3.6

PR:             ports/122607
Submitted by:   maintainer (Fernan Aguero)
30 Mar 2008 05:07:37
Original commit files touched by this commit  35.3.5
rafan search for other commits by this committer
- Update to 35.3.5
- 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)
09 Mar 2007 11:26:13
Original commit files touched by this commit  34.26.2
miwi search for other commits by this committer
- Update to 34.26.2

PR:             110079
Submitted by:   Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)
31 Oct 2006 09:02:04
Original commit files touched by this commit  34.t26.b3
miwi search for other commits by this committer
- Update to 34.t26.b3

PR:             ports/104508
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
09 Jun 2006 19:18:08
Original commit files touched by this commit  34.t25.d9
pav search for other commits by this committer
- Update to 34.t25.d9

PR:             ports/98761
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
05 Jun 2006 21:18:24
Original commit files touched by this commit  34.t25.d8
erwin search for other commits by this committer
- Update to 34.t25.d8 [1]
- While I'm here, pet portlint [2]

PR:             98398 [1]
Submitted by:   miwi [1], self [2]
Approved by:    maintainer [1]
24 May 2006 16:55:46
Original commit files touched by this commit  34.t25.d7
sem search for other commits by this committer
- update to 34.t25.d7
- add MASTER_SITE_LOCAL as a second master site

PR:             ports/97310
Submitted by:   maintainer
21 May 2006 21:32:08
Original commit files touched by this commit  34.t25.d6
kris search for other commits by this committer
BROKEN: Unfetchable
07 May 2006 16:52:33
Original commit files touched by this commit  34.t25.d6
sem search for other commits by this committer
- Update to 34.t25.d6

PR:             ports/96063
Submitted by:   maintainer
20 Mar 2006 22:23:24
Original commit files touched by this commit  34.t25.d5
pav search for other commits by this committer
- Update to 34.t25.d5

PR:             ports/94741
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
10 Feb 2006 09:37:02
Original commit files touched by this commit  34.t25.d4
lawrance search for other commits by this committer
Update to 34.t25.d4.

PR:             ports/93052
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
22 Jan 2006 08:20:34
Original commit files touched by this commit  33.t08.d4
edwin search for other commits by this committer
SHA256ify

Approved by:    krion@
01 Jul 2004 03:02:23
Original commit files touched by this commit  33.t08.d4
linimon search for other commits by this committer
Chase mastersite and fix checksum to unbreak.  (Changes are inclusion of a
logfile, one Linux-only change, and one change in a test script).  Assign
submitter as new maintainer as current one has not responded to PRs for
some time.

PR:             ports/68199
Submitted by:   Fernan Aguero <fernan at iib dot unsam dot edu dot ar>
21 Jun 2004 21:27:46
Original commit files touched by this commit  33.t08.d4
kris search for other commits by this committer
Set an expiry date of 2004-08-20 for these BROKEN/IGNORE/FORBIDDEN
ports.  They will be removed on or after that date if they are still
broken and no fix has been submitted to GNATS.
31 Mar 2004 03:12:58
Original commit files touched by this commit  33.t08.d4
trevor search for other commits by this committer
SIZEify (maintainer timeout)
21 Feb 2004 19:31:10
Original commit files touched by this commit  33.t08.d4
kris search for other commits by this committer
BROKEN: Checksum mismatch
15 Nov 2003 20:13:21
Original commit files touched by this commit  33.t08.d4
marcus search for other commits by this committer
unPERLify by using REINPLACE_CMD and SED where appropriate.

PR:             47654
Submitted by:   Simon 'portlint' Schubert <corecode@corecode.ath.cx>
22 Oct 2003 09:29:55
Original commit files touched by this commit  33.t08.d4
osa search for other commits by this committer
Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992
07 Mar 2003 05:56:43
Original commit files touched by this commit  33.t08.d4
ade search for other commits by this committer
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.
23 Aug 2002 03:36:33
Original commit files touched by this commit  33.t08.d4
kris search for other commits by this committer
Prefer <limits.h> over <values.h> as the latter has been removed from
-current.

Noticed by:     bento
03 Jul 2001 10:08:26
Original commit files touched by this commit
wjv search for other commits by this committer
Replace erroneous usage of INSTALL_MAN with INSTALL_DATA.    
27 Jun 2001 11:15:02
Original commit files touched by this commit
wjv search for other commits by this committer
Updating my email address in my remaining ports.    
07 May 2001 13:16:33
Original commit files touched by this commit
jeh search for other commits by this committer
Updata biology/fasta3 to version 33.t08.d4    
22 Mar 2001 09:04:47
Original commit files touched by this commit
sobomax search for other commits by this committer
Update to 33.t08.d3.    
12 Mar 2001 10:24:38
Original commit files touched by this commit
nbm search for other commits by this committer
- A small bugfix lead to a rerelease without a version number change.   - Bumped
PORTREVISION.    
08 Mar 2001 14:39:17
Original commit files touched by this commit
sf search for other commits by this committer
update to 33.t08.d2.    
11 Feb 2001 16:29:00
Original commit files touched by this commit
jeh search for other commits by this committer
- 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)    

Number of commits found: 45

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