and thoroughly tested framework for: controlling third-party applications;
devising workflows; querying databases; conducting novel probabilistic
analyses of biological sequence evolution; and generating publication quality
graphics. It is distinguished by many unique built-in capabilities (such as
true codon alignment) and the frequent addition of entirely new methods for
the analysis of genomic data.
WWW: http://pycogent.sourceforge.net/
PR: ports/135863
Submitted by: Wen Heping <wenheping at gmail.com>
modular xorg.
- supply corresponding USE_XORG for all imake-using ports that need it
- USE_IMAKE no longer implies USE_XLIB in absence of USE_XORG
- retire USE_X_PREFIX which is not really used anywhere after the
above change
- a few minor nits like whitespace and SF macro
Tested by: 2 tinderbox runs by pav
Approved by: portmgr (pav)
2009-05-31 biology/p5-bioperl-run-devel: no longer under development
2009-06-01 net-p2p/deluge05: use net-p2p/deluge instead
2009-06-03 textproc/gmat: failed to build for a long time, no maintainer and apparently no users either
manipulate, translate, and validate SBML files and data streams. It is
not an application itself (though it does come with example programs),
but rather a library you can embed in your own applications.
LibSBML understands all Levels and Versions of SBML, as well as the
SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in
ISO C and C++ but can be used from all the languages listed in the
right-hand box.
WWW: http://www.sbml.org/
PR: ports/135022
Submitted by: Wen Heping <wenheping at gmail.com>
through its REST web service (http://www.g-language.org). This module
allows almost everything G-language GAE can do, without installing
all necessary tookits and modules.
Advantage of this module over the standard installation of
G-language GAE package is:
1. Easy installation from CPAN
2. Extremely light-weight (less than 1000 lines of code)
3. Does not require much CPU/RAM (all calculation is done on
the cloud)
Disadvantages includes:
1. Slower analysis speed
2. Internet connection is required
3. No other software interfaces such as the G-language Shell
WWW: http://search.cpan.org/dist/Bio-Glite/
PR: ports/133273
Submitted by: Wen Heping <wenheping at gmail.com>
both current (fc4) and future linux (f8) distributions at one
ports tree.
The patch contains full changes to ports/Mk files and all ports involved.
But only infrastructure is changed. The resulting packages are the same as
before. Hence no need to bump PORTREVISIONs.
The idea was taken from bsd.gnome.mk and others.
More than 130 ports are switched to follow a new linux infrastructure
introduced by changes to bsd.port.mk, bsd.linux-rpm.mk and a new
bsd.linux-apps.mk.
Thanks for all who was involved and helped me with this work.
And help from Alexander Leidinger was incredible.
Other changes are coming. Stay tuned!
PR: ports/132510
Submitted by: bsam (me)
Exp-run by: portmgr (pav)
- Bump PORTREVISION for all ports depending on libglut since the shlib
version number went from 4 to 3.
- Bump PORTREVISION for all ports depending on libXaw as libXaw.so.8 isn't
installed anymore.
- Couple of ports fixes (mostly missing xorg components added to USE_XORG).
