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  1. Title 0.9.8.7_beta_1
  2. Release 0.9.8.7_beta_1
  3. Link bpipe-0.9.8.7_beta_1.tar.gz


  4. =========== Changes for Bpipe Version 0.9.8.7_beta_1 ============
    
       - avoid encoding whole directory path into internal property
         file names (file path too long errors) 
        
       - fix parent branches not visible in children via 
         branch property 
        
       - fix method missing error when multiplying by map by list 
        
       - Reformatting and summarizing of errors at end of pipeline to
         make it easier to see where & why pipelines failed 
    
       - Aggregating identical errors from multiple branches together
         in output so that failures from many branches are less
         verbose 
    
       - Support for 'load' within a pipeline stage.  Loads
         into the context of current branch rather than global.
         Pipeline stages not supported 
        
       - prevent error if files
         used by Bpipe are not writable but are deletable 
        
       - prevent premature wildcard expansion of quoted arguments passed to
         Bpipe, prevent error if internal files used by Bpipe are not
         writable but are deletable 
        
       - support for cleanup as
         command in pipeline stage 
        
       - refactor launching in
         different modes to use common code 
        
       - add more info to
         started event 
        
       - attempt to ensure log messages written
         even if exit due to outofmemory error 
        
       - reinstate 'STARTED' event as part of getting web 
         interface going again
    
       - log message if file is not cleaned up because it doesn't
         exist: help to diagnose problems with files not cleaned up 
       
       - better log info about where config files are 
        
       - allow memory to be integer for torque/slurm/etc, fix error
         querying status in torque/slurm/etc, include queuing system
         command id in bpipe status output 
        
       - show pending and waiting jobs with bpipe status, don't throw ugly error 
         if no commands ever run 
        
       - Fix: downstream references to inputs
         by index throwing "expected more inputs" error incorrectly 
       
       - avoid confusing stack overflow when user defines branch
         variable with same name as pipeline stage 
        
       - accept 'MB' or 'GB' in command line option for memory,
         cache runtime directory instead of creating new File objects
         all the time to figure it out 
        
       - Merge pull request #123
         from lonsbio/master 
        
       - prevent null pointer exception when list containing null 
         provided to 'from' 
       
       - fix multiple inputs not
         forwarding correctly when referenced using "$inputs" 
        
       - Merge pull request #122 from druvus/master 
        
       - Bug fixes for lsf 
        
       - Added walltime option for Lsf 
        
       - caching of DAG lookups by
         canonical path to speed up large, complex pipelines 
        
       - caching of canonical path with check of basePath to ensure
         consistency 
        
       - some initial, untested support for caching
         DAG graph lookups to speed up large pipelines 
        
       - fix dependency issues after
         cleanup when non-default output directory used 
        
       - Performance optimisations for systems where canonicalPath is
         very slow, better logging to resolve dependency issues