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ChangeLog
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2017-09-27 Claude Lepage <claude@bic.mni.mcgill.ca>
* add environment for Slurm Work Scheduler
* bumped version to 0.8.3
2014-10-30 Claude Lepage <claude@bic.mni.mcgill.ca>
* exclude environment variables with () in them (see bash CentOS-6)
from sge.pm and pbs.pm. Not sure if this is 100% safe, but it works.
* bumped version to 0.8.2
2013-11-08 Claude Lepage <claude@bic.mni.mcgill.ca>
* little fixes in sge.pm and pbs.pm to make subsetToStage work properly
(don't execute stage after the To stage)
* fix packaging for 'make dist' to work
* bumped version to 0.8.1
2012-01-31 Claude Lepage <claude@bic.mni.mcgill.ca>
* added function setCommand to use qsub or msub
* bumped version to 0.8.0
2009-02-27 Claude Lepage <claude@bic.mni.mcgill.ca>
* added function resetAfterStage
2008-06-12 Jason Lerch <jason@phenogenomics.ca>
* added PMPDB - a subclass of PMP which keeps track of status
information inside a sqlite database.
* added PMPDB pod documentation.
2008-02-19 Claude Lepage <claude@bic.mni.mcgill.ca>
* allow jobs scripts over 100k (sh max command line size)
by using a tmp file
2007-09-14 Claude Lepage <claude@bic.mni.mcgill.ca>
* fixed syntax error in PMP.pm for createFilenameDotGraph and
added stage sort in createDotGraph
2007-08-24 Claude Lepage <claude@bic.mni.mcgill.ca>
* fixed syntax error with `touch` in sge.pm and pbs.pm
2007-06-05 Claude Lepage <claude@bic.mni.mcgill.ca>
* added granularity option for running stages all in
all script at once
* added global options for qsub for site-specific rules
* fixed a bug with in: and out:
2007-01-17 Jason Lerch <jason@bic.mni.mcgill.ca>
* some documentation updates.
* removed one superfluous print statement from PMP.pm.
2007-01-17 Jason Lerch <jason@bic.mni.mcgill.ca>
* added check to run() for whether non-existent inputs to file
exist iniside PMP.pm.
* added sge_opts as allowable stage specifiction checked in sge.pm
* added test for non-existent files.
* added test for requested memory to sge.pm
2007-01-11 Jason Lerch <jason@bic.mni.mcgill.ca>
* added ability to define inputs and outputs from within the
stages parameter.
* added a test-case for that scenario.
2007-01-11 Claude Lepage <claude@bic.mni.mcgill.ca>
* improve management of lock files
* return control to calling program when a failure occurs instead
of abruptly terminating (and delete locks too)
2007-01-10 Jason Lerch <jason@bic.mni.mcgill.ca>
* added new function to compute dependencies based on inputs and outputs.
* fixed DOT file creation to remove periods from stage names.
* repeat of output now dies in computeDependenciesFromInputs.
2007-01-05 Jason Lerch <jason@bic.mni.mcgill.ca>
* fixed the pmp_test.t to use PMP::spawn interface
* added lock cleaning and initing to pmp_test.t
* fixed how pmp_sge_test.t checks for SGE existence
* pmp_prereqs_test.t now expects to fail with erroneous prereq.
2006-11-04 Claude Lepage <claude@bic.mni.mcgill.ca>
* add cleanup() to delete lock files on an interrupt (Alex Z)
* add maximum number of queued jobs (Alex Z)
* bumped version to 0.7.0
2006-04-06 Claude Lepage <claude@bic.mni.mcgill.ca>
* remove default queues in sge and pbs
* implementation of project lock files
* bumped version to 0.6.9
2006-04-06 Claude Lepage <claude@bic.mni.mcgill.ca>
* add hierarchical dependencies on prereqs for restarts
* add priority scheme to sge (same as pbs)
* bumped version to 0.6.8
2006-04-06 Claude Lepage <claude@bic.mni.mcgill.ca>
* fix shellquote for sge and pbs for args with quotes
* create own module for spawn.pm
* bumped version to 0.6.7
2006-03-08 Claude Lepage <claude@bic.mni.mcgill.ca>
* incorporated Sebastien's change for sge queue system
* bumped version to 0.6.6
2004-10-08 Jason Lerch <jason@bic.mni.mcgill.ca>
* bumped version to 0.6.5
* incorporated Oleg's bug fixes
* added sge_test to CVS repository.
* added AUTHORS file.
2004-10-07 Jason Lerch <jason@bic.mni.mcgill.ca>
* added missing methods to the various POD files.
* fixed bug in resetFromStage - the regex in grep were incorrect
when the stagename was a partial version of another stage,
i.e. "pve" and "pve_curvature".
2004-10-01 Jason Lerch <jason@bic.mni.mcgill.ca>
* fixed createFilenameDotGraph so that it now produces sensible
pictures.
2004-09-30 Jason Lerch <jason@bic.mni.mcgill.ca>
* bumped version to 0.6.1
* skips SGE test if qsub not present in path
* fixed a bug in PMP::updateStageStatus
2004-09-29 Jason Lerch <jason@bic.mni.mcgill.ca>
* added a class to submit jobs through the Sun Grid Engine
* added a test for the sge submission system
* bumped version to 0.6
2004-09-17 Jason Lerch <jason@bic.mni.mcgill.ca>
* now allows for non-existent prereqs as well as empty prereq arrays.
* some extra tests added
* version bumped to 0.5
2004-08-16 Jason Lerch <jason@bic.mni.mcgill.ca>
* added ability to use only a subset of stages. Not the greatest
implementation yet, as inclusion of siblings in the stage
hierarchy is arbitrary. Only a single to stage can be specified at
this point in time.
2004-08-04 Jason Lerch <jason@bic.mni.mcgill.ca>
* added pipeline status report printing functions
2004-08-01 Jason Lerch <jason@bic.mni.mcgill.ca>
* added Makefile.PL
* moved lots of files around to make it compatible with the usual
installation procedure.
* renamed files so that they install as, for example, PMP::array
2004-07-31 Jason Lerch <jason@bic.mni.mcgill.ca>
* added methods to print a CSV separated status file. Both PMP.pm
and PMParray are affected.
2004-06-11 Jason Lerch <jason@bic.mni.mcgill.ca>
* added this ChangeLog file
* changed the way shellquoting is handled: it is now not done by
default, but has to specified in addStage.