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Port details
ncbi-toolkit 2012.06.20 biology on this many watch lists=2 search for ports that depend on this port
NCBI development toolkit, including BLAST 2 and GenBank/Entrez support

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 29 Oct 2000 10:56:24
License: not specified in port


The NCBI (National Center for Biotechnology Information) development toolkit,
containing various libraries needed by NCBI applications, as well as a
software suite containing, amongst other things, NCBI BLAST 2.0.

From the README:

  The NCBI Software Development Toolkit was developed for the production and
  distribution of GenBank, Entrez, BLAST, and related services by NCBI. We
  make it freely available to the public without restriction to facilitate
  the use of NCBI by the scientific community. However, please understand
  that while we feel we have done a high quality job, this is not commercial
  software.

  The documentation lags considerably behind the software and we must make
  any changes required by our data production needs. Nontheless, many people
  have found it a useful and stable basis for a number of tools and
  applications.

WWW: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html
SVNWeb : Main Web Site : Distfiles Availability : PortsMon

NOTE: FreshPorts displays only required dependencies information. Optional dependencies are not covered.

Required To Build:
  1. x11/libXpm
Required To Run:
  1. x11/libXpm
Required Libraries:
  1. converters/libiconv
  2. x11-toolkits/open-motif

This port is required by:

for Build * - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...

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


Configuration Options
===> The following configuration options are available for ncbi-toolkit-2012.06.20:
     DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings

Master Sites:
  1. ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/ncbi-toolkit-2012.06.20/
  2. ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/20120620/

Number of commits found: 40

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
23 Mar 2014 20:50:54
Original commit files touched by this commit  2012.06.20
Revision:348888
pawel search for other commits by this committer
Add staging support
20 Sep 2013 15:55:44
Original commit files touched by this commit  2012.06.20
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)
04 Sep 2013 18:06:08
Original commit files touched by this commit  2012.06.20
Revision:326307
madpilot search for other commits by this committer
- Make ports use the libc provided iconv implementation on 10-CURRENT
  after r254273
- Fix a bunch of ports to properly work after this
- Mark converters/libiconv as IGNORE for systems with iconv in libc

Reviewed by:	bapt
Approved by:	portmgr (bapt)
Discussed with:	bapt, bsam (who both contributed ideas and code)
09 Jul 2013 21:49:36
Original commit files touched by this commit  2012.06.20
Revision:322587
bapt search for other commits by this committer
Convert from USE_MOTIF to USES=motif
While here:
- trim headers
- Remove indefinite article from comment
- convert USE_GMAKE to USES=gmake
14 Mar 2013 05:27:58
Original commit files touched by this commit  2012.06.20
Revision:314129
miwi search for other commits by this committer
- Update to 2012.06.20

PR:		176544
Submitted by:	Ports Fury
01 Oct 2012 14:45:17
Original commit files touched by this commit  2009.03.01_1
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  2009.03.01_1
eadler search for other commits by this committer
- remove maintainer tags from pkg-descr

Approved by:    portmgr
Approved by:    bapt (mentor)
02 May 2011 12:41:44
Original commit files touched by this commit  2009.03.01_1
makc search for other commits by this committer
Fix build with open-motif-2.3.3

PR:             ports/154044
Submitted by:   Mikhail Tsatsenko <m.tsatsenko at gmail.com>
Exp-runs by:    pav
19 Mar 2011 12:38:54
Original commit files touched by this commit  2009.03.01
miwi search for other commits by this committer
- Get Rid MD5 support
31 Jan 2010 03:42:20
Original commit files touched by this commit  2009.03.01
pgollucci search for other commits by this committer
- use $SUB_FILES to dynamically adjust pkg-message

PR:             ports/142408
Submitted by:   Sevan Janiyan <venture37@geeklan.co.uk>
Approved by:    fernan@iib.unsam.edu.ar (maintainer)
28 Mar 2009 16:59:39
Original commit files touched by this commit  2009.03.01
miwi search for other commits by this committer
- Update to 2009.03.01

PR:             133099
Submitted by:   Fernan Aguero <fernan.aguero@gmail.com>
Approved by:    maintainer
19 Apr 2008 17:56:05
Original commit files touched by this commit  2006.05.07_1
  Sanity Test Failure
miwi search for other commits by this committer
- Remove unneeded dependency from gtk12/gtk20 [1]
- 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)
19 May 2007 20:32:57
Original commit files touched by this commit  2006.05.07_1
flz search for other commits by this committer
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
09 Dec 2006 07:48:18
Original commit files touched by this commit  2006.05.07
rafan search for other commits by this committer
- Respect X11BASE

Approved by:    portmgr (linimon)
06 Jun 2006 12:05:19
Original commit files touched by this commit  2006.05.07
itetcu search for other commits by this committer
Update biology/ncbi-toolkit to the latest release.
Quoting from www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml
Major changes include:
 blastall now uses the new engine by default, resulting
 in significant performance improvements and enabling
 query concatenation for all program types.

PR:             ports/98570
Submitted by:   maintainer
Approved by:    lawrance (mentor, implict)
22 Jan 2006 01:25:24
Original commit files touched by this commit  2005.12.06
edwin search for other commits by this committer
Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtry

Approved by:    krion@
PR:             ports/88711 (related)
14 Jan 2006 19:34:43
Original commit files touched by this commit  2005.12.06
pav search for other commits by this committer
- Update to 2005.12.06

PR:             ports/91714
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
11 Oct 2005 22:33:35
Original commit files touched by this commit  2005.06.05
sem search for other commits by this committer
- Update to 20050605

PR:             ports/87266
Submitted by:   maintainer
14 Sep 2005 09:24:04
Original commit files touched by this commit  2004.10.20_1
vs search for other commits by this committer
Don't strip static libraries on installation ;)
(Unbreaks e.g. biology/nclever)
20 Mar 2005 11:47:59
Original commit files touched by this commit  2004.10.20
pav search for other commits by this committer
- Fix man page damage I did last night

Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
19 Mar 2005 21:32:13
Original commit files touched by this commit  2004.10.20
pav search for other commits by this committer
- Update to 2.2.10 from 20041020
- Transfer maintainership

PR:             ports/67735
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
Approved by:    old maintainer indirectly in
http://lists.freebsd.org/pipermail/freebsd-ports-bugs/2004-June/035351.html
01 Nov 2004 22:21:02
Original commit files touched by this commit  2004.06.16
pav search for other commits by this committer
- Update to 2004.06.16

Inspired by:    ports/72726
Approved by:    maintainer timeout (2 weeks)
13 Nov 2003 14:45:08
Original commit files touched by this commit  2003.04.21
trevor search for other commits by this committer
Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.
22 Oct 2003 09:29:55
Original commit files touched by this commit  2003.04.21
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
05 May 2003 12:24:08
Original commit files touched by this commit  2003.04.21
arved search for other commits by this committer
Update to 2003.04.21

PR:             51709
Submitted by:   Tony Maher <tonymaher@optushome.com.au>
21 Feb 2003 11:01:38
Original commit files touched by this commit  2002.04.26
knu search for other commits by this committer
De-pkg-comment.
21 Sep 2002 14:56:18
Original commit files touched by this commit  2002.04.26
ijliao search for other commits by this committer
add forgotten "USE_REINPLACE=yes"

Submitted by:   maintainer
21 Sep 2002 06:59:28
Original commit files touched by this commit  2002.04.26
ijliao search for other commits by this committer
upgrade to 20020426

PR:             39357
Submitted by:   maintainer
08 Jun 2002 00:40:10
Original commit files touched by this commit  2001.12.20
petef search for other commits by this committer
Correct MASTER_SITES.

PR:             39016
Submitted by:   maintainer
22 Feb 2002 07:57:07
files touched by this commit
pat search for other commits by this committer
Update to 2001.12.20    
19 Sep 2001 14:03:18
files touched by this commit
wjv search for other commits by this committer
- Add installation of include files   - Bump PORTREVISION    
06 Aug 2001 11:50:02
files touched by this commit
wjv search for other commits by this committer
Update maintainer's email address.    
10 Jul 2001 17:35:08
files touched by this commit
fenner search for other commits by this committer
Update Tony Maher's email address.    
20 Jun 2001 15:25:55
files touched by this commit
wjv search for other commits by this committer
Update to version 2001.04.03; add installation of some documentation.    
18 Dec 2000 20:32:56
files touched by this commit
demon search for other commits by this committer
Remove trailing period and package name from the pkg-comment.    
15 Nov 2000 00:54:09
files touched by this commit
jeh search for other commits by this committer
They made changes to the "blast" program.    
07 Nov 2000 23:28:20
files touched by this commit
asami search for other commits by this committer
Change motif to a normal dependency.  REQUIRES_MOTIF is now called   USE_MOTIF
and generates a LIB_DEPENDS to x11-toolkits/open-motif.  As   before, it implies
USE_XPM (and therefore USE_XLIB).  Motif-dummy is   removed from
PKG_IGNORE_DEPENDS, whose sole resident is now XFree86-3.    
03 Nov 2000 13:23:15
files touched by this commit
jeh search for other commits by this committer
Yes.  They did re-roll this version, it is legit.   They donot version the dist,
but store them in versioned dir.  Update    Makefile to handle that.   Update
CHECKSUM    
02 Nov 2000 11:25:50
files touched by this commit
jeh search for other commits by this committer
Updated to new version.  That is the pits, the day after it becomes   a port
they release a new version.  This is a new version, w/o a number.    
29 Oct 2000 13:56:24
files touched by this commit
jeh search for other commits by this committer
New Port: biology/ncbi-toolkit   National Center for Biotechnology Information
(NCBI) Development Toolkit.    

Number of commits found: 40

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