ncbi-toolkit 2006.05.07_1 biology =3

NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
Maintained by: fernan@iib.unsam.edu.ar
Port Added: 29 Oct 2000 10:56:24

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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 <tonym@biolateral.com.au>

WWW: http://www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon

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Required To Build: x11/libXpm
Required To Run: x11/libXpm
Required Libraries: x11-toolkits/open-motif

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

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Configuration Options

     No options to configure

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Master Sites:

ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/20060507/

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/ncbi-toolkit-2006.05.07/

- 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)

- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.

- Respect X11BASE

Approved by:    portmgr (linimon)

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)

Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtry

Approved by:    krion@
PR:             ports/88711 (related)

- Update to 2005.12.06

PR:             ports/91714
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

- Update to 20050605

PR:             ports/87266
Submitted by:   maintainer

Don't strip static libraries on installation ;)
(Unbreaks e.g. biology/nclever)

- Fix man page damage I did last night

Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

- 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

- Update to 2004.06.16

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

Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.

Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992

Update to 2003.04.21

PR:             51709
Submitted by:   Tony Maher <tonymaher@optushome.com.au>

De-pkg-comment.

add forgotten "USE_REINPLACE=yes"

Submitted by:   maintainer

upgrade to 20020426

PR:             39357
Submitted by:   maintainer

Correct MASTER_SITES.

PR:             39016
Submitted by:   maintainer

Update to 2001.12.20    

- Add installation of include files   - Bump PORTREVISION    

Update maintainer's email address.    

Update Tony Maher's email address.    

Update to version 2001.04.03; add installation of some documentation.    

Remove trailing period and package name from the pkg-comment.    

They made changes to the "blast" program.    

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.    

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    

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.    

New Port: biology/ncbi-toolkit   National Center for Biotechnology Information
(NCBI) Development Toolkit.    

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