The FreeBSD Ports Archive

FreeBSD biology : ncbi-toolkit

NCBI development toolkit, including BLAST 2 and GenBank/Entrez support

 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.

-- Tony Maher  

ncbi-toolkit history

v. 1.25
date: 2007/05/19 20:00:24;  author: flz;  state: Exp;  lines: +1 -0
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.

v. 1.24
date: 2006/12/09 07:48:18;  author: rafan;  state: Exp;  lines: +5 -0
- Respect X11BASE

Approved by:	portmgr (linimon)

v. 1.23
date: 2006/06/06 12:05:19;  author: itetcu;  state: Exp;  lines: +1 -1
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)

v. 1.22
date: 2006/01/14 19:34:43;  author: pav;  state: Exp;  lines: +5 -5
- Update to 2005.12.06

PR:		ports/91714
Submitted by:	Fernan Aguero  (maintainer)

v. 1.21
date: 2005/10/11 22:33:34;  author: sem;  state: Exp;  lines: +12 -13
- Update to 20050605

PR:		ports/87266
Submitted by:	maintainer

v. 1.20
date: 2005/09/14 09:24:04;  author: vs;  state: Exp;  lines: +2 -1
Don't strip static libraries on installation ;)
(Unbreaks e.g. biology/nclever)

v. 1.19
date: 2005/03/20 11:47:59;  author: pav;  state: Exp;  lines: +9 -7
- Fix man page damage I did last night

Submitted by:	Fernan Aguero  (maintainer)

v. 1.18
date: 2005/03/19 21:32:13;  author: pav;  state: Exp;  lines: +75 -26
- Update to 2.2.10 from 20041020
- Transfer maintainership

PR:		ports/67735
Submitted by:	Fernan Aguero  (maintainer)
Approved by:	old maintainer indirectly in
http://lists.freebsd.org/pipermail/freebsd-ports-bugs/2004-June/035351.html

v. 1.17
date: 2004/11/01 22:21:01;  author: pav;  state: Exp;  lines: +4 -4
- Update to 2004.06.16

Inspired by:	ports/72726
Approved by:	maintainer timeout (2 weeks)

v. 1.16
date: 2003/11/13 14:44:58;  author: trevor;  state: Exp;  lines: +1 -1
Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.

v. 1.15
date: 2003/05/05 12:24:07;  author: arved;  state: Exp;  lines: +1 -7
Update to 2003.04.21

PR:		51709
Submitted by:	Tony Maher 

v. 1.14
date: 2003/02/21 11:01:35;  author: knu;  state: Exp;  lines: +1 -0
De-pkg-comment.

v. 1.13
date: 2002/09/21 14:56:18;  author: ijliao;  state: Exp;  lines: +1 -0
add forgotten "USE_REINPLACE=yes"

Submitted by:	maintainer

v. 1.12
date: 2002/09/21 06:59:27;  author: ijliao;  state: Exp;  lines: +2 -2
upgrade to 20020426

PR:		39357
Submitted by:	maintainer

v. 1.11
date: 2002/06/08 00:40:10;  author: petef;  state: Exp;  lines: +1 -1
Correct MASTER_SITES.

PR:		39016
Submitted by:	maintainer

v. 1.10
date: 2002/02/22 07:57:05;  author: pat;  state: Exp;  lines: +11 -14
Update to 2001.12.20

PR:		35203
Submitted by:	maintainer

v. 1.9
date: 2001/09/19 13:03:17;  author: wjv;  state: Exp;  lines: +2 -1
- Add installation of include files
- Bump PORTREVISION

PR:		30660
Submitted by:	Tony Maher  (MAINTAINER)

v. 1.8
date: 2001/08/06 10:50:02;  author: wjv;  state: Exp;  lines: +2 -2
Update maintainer's email address.

Approved by:	MAINTAINER

v. 1.7
date: 2001/07/10 16:35:08;  author: fenner;  state: Exp;  lines: +2 -2
Update Tony Maher's email address.

v. 1.6
date: 2001/06/20 14:25:52;  author: wjv;  state: Exp;  lines: +12 -4
Update to version 2001.04.03; add installation of some documentation.

Approved by:	MAINTAINER

v. 1.5
date: 2000/11/15 00:54:09;  author: jeh;  state: Exp;  lines: +3 -2
They made changes to the "blast" program.

Submitted by:	MAINTAINER

v. 1.4
date: 2000/11/07 23:27:55;  author: asami;  state: Exp;  lines: +2 -2
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.

Most of the simple ".if defined(HAVE_MOTIF)"s are removed to always
have USE_MOTIF.  ftp/moxftp will define USE_MOTIF unless
WANT_ATHENA_VERSION (new variable) is defined.  I merged the X cases
in cad/mars, so USE_MOTIF is used iff WITHOUT_X11 is not defined.

I will remove x11-toolkits/Motif-dummy (which has been repo copied to
open-motif) in a few days.

v. 1.3
date: 2000/11/03 13:23:15;  author: jeh;  state: Exp;  lines: +2 -2
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

Submitted by:	bento

v. 1.2
date: 2000/11/02 11:25:41;  author: jeh;  state: Exp;  lines: +2 -2
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.

PR:		22522
Submitted by:	Tony Maher  MAINTAINER

v. 1.1
date: 2000/10/29 13:56:23;  author: jeh;  state: Exp;
New Port: biology/ncbi-toolkit
National Center for Biotechnology Information (NCBI) Development Toolkit.

PR:		22388
Submitted by:	Tony Maher 
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