[Segway-announce] Segway 1.2.0 released

Eric Roberts eroberts at uhnresearch.ca
Fri Aug 29 09:02:22 PDT 2014

We are pleased to announce the availability of Segway 1.2.0.

Segway has now been brought up to date with Python, Genomedata, and all
of it's dependencies. Most notably it now includes support for running
locally (without a cluster), runs on Torque, and features support for
sub-segment labels thanks to the efforts of Adam Shaw. The installation
process is also much simpler so upgrading should be relatively painless.

Please let me know if you have any comments on Segway, its
documentation, web site, installation, or anything else. (The
preferred place to make these comments is on the segway-users mailing
list or by reporting an issue on the issue tracker, both linked from
the main web site).

Here is a full list of changes made since the last announcement here:


Known Issues:

* Segway will produce incorrect segmentations if the
tracks are not specified in the order they appear in the genomedata
archive providing the data.
* Segway --version will print "$Revision$". This is a specific SVN
migration issue.

Updated Requirements:

* now requires Python >=2.6 (released 6 years ago) and <=3.0
(although we will switch to Python 2.7 when we need it, so if you
are upgrading, go all the way now)
* now requires Genomedata >=1.3.1
* now requires the newest release of GMTK (1.0.1 or >= 1.0.0 80c1d70cea9d
(ticket161-2) for increased speed)

Major Features:

* segway: now has experimental support for running without any cluster
system or drmaa. By default if nothing is available, or use
SEGWAY_CLUSTER (thanks to Max Libbrecht)
* segway: now has experimental Torque support. PBS and PBS Pro will
probably work with some changes--please e-mail Michael if you want
to help with identifying the necessary changes (thanks to Jay

Minor Features:

* segway: made matching against unmodified vs. modified partitions
output from
gmtk more lenient to match against
* segway: SEGWAY_CLUSTER environment variable allows manual
specification of a cluster system (e.g. export SEGWAY_CLUSTER=local)
* segway: new escaping method from Genomedata tracknames to GMTK
tracknames allows any arbitrary Genomedata trackname, but this means
that previous files will be incompatible, since "_" is now replaced
by "_5F" and "." by "_2E" (formerly both of these were "_", which
was ambiguous)
* segway: allow concatenated segmentation of tracks with --trackname
track1,track2, which gives you only one set of parameters. you may
need to adjust existing train.tab files to use track_specs instead
of include_tracknames because of other necessary changes
* segway-layer: add --bigBed option, which works if you have
bedToBigBed in your path
* segway: add --bigBed option which calls segway-layer --bigBed
* segway-layer: add --no-recolor option which doesn't override colors at all
* segway: add --output-label option to control segmentation output when
using sublabels
* segway: segway.sh has cd command in addition to segway command

Bug Fixes:

* segway: LSF: fix bug where wrapper script sometimes did not delete
temporary observation files after a crash
* segway: LSF: no longer generates mktemp warning messages
* segway-layer: fix issue #19. Now doesn't override previous colors
when mnemonics aren't supplied (thanks to Jay Hesselberth)
* segway-winner: fix issue #21. Now works on Python 2.5.1 (but you
should be using 2.6 or later anyway)
* segway: semi-supervised mode no longer causes assertion error
* segway: posterior task now compatible with sublabel output mode


* default setuptools version now 0.6c11
* segway: more informative error message when supervision labels overlap
each other
* segway: MC/MX/REAL_MAT direct parameters are no longer trained
(MEAN/COVAR/DENSECPT parameters are)
* segway: removes PYTHONINSPECT from environment for sub-tasks, which
caused identify mode failures before
* segway: some changes in the way structure files work
* installation: always require drmaa. setuptools extras_require wasn't
that useful in practice
* installation: include SLURM support if you have drivers/slurm.py installed
* test: run pyflakes first
* test: use fixed random seed to generate input.master every time
* test: when files differ, output is in a form that makes it easier to diff
* test: update for new GMTK
* prereqs: hgtools is now a prerequisite (but only installed to local
segway directory)

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