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  1. Title bpipe-0.9.9.3
  2. Release 0.9.9.3
  3. Link bpipe-0.9.9.3.tar.gz


  4. # Bpipe Version 0.9.9.3
    
    ##  Summary
    
    Bpipe 0.9.9.3 contains a large number of bug fixes that affect 
    specific scenarios where unexpected behavior was being encountered. It also includes
    some major enhancements including the ability to "pause" and resume a pipeline
    without stopping in-progress jobs, and also support for pre-allocating 
    resources when running pipelines in environments where resources can
    take time become available after they are requested. The new 'bpipe jobs'
    command is also worth a look, especially the 'bpipe jobs -watch' option.
    
    [Download](http://download.bpipe.org/versions/bpipe-0.9.9.3.tar.gz)
    
    ## Highlights
    
    ### Enhancements
    
     * Support for preallocated resources for commands and allocated compute resources that 
       persist between pipeline invocations. See the [documentation](http://docs.bpipe.org/Guides/PreallocatedJobs/)
       for more details.
    
     * Support for using Groovy Grab/Grape to add libraries to pipeline
       (see [documentation](http://docs.bpipe.org/Guides/ExtendingClassPath/))
    
     * Improved output to 'bpipe query' 
    
     * Greatly enhanced, real time display for 'bpipe jobs'
    
     * More informative display from 'bpipe status'
    
     * Generic custom options for queuing system jobs (see #193)
    
     * Improved behavior of stop and status when no pipeline running
    
     * Support to 'pause' a running pipeline via 'bpipe pause'
    
     * Tools can be located relative to pipeline for purpose of version probing
    
     * Experimental support for inline python, sqlite and groovy commands
    
     * Support to remake specific files via bpipe remake <files>
    
     * Ability to split genomes into arbitrary sized parts specified in bases
    
     * Support for syntax of form ${output.withFlag("--someFlag")}
    
    
    ### Bugfixes
    
     * Fix torque executor printing spurious errors when stopping jobs
    
     * fix spurious error produced by torque module request
    
     * Fix #209 - torque mem param variable missing in some situations
    
     * Fix sbatch/qsub failures not recognised correctly, producing
       misleading errors
    
     * Fix: files in output dirs not cleaned up if command fails
    
     * Fix #199: Stop command not halting jobs on some clusters
    
     * Fix timeout not treated as failure under SLURM
    
     * Fix split pattern on symbolic links in directory not resolving
    
     * Fix $outputs.ext (multiple outputs based on extension) broken
    
     * Fix genomes lacking 'chr' prefix not supported by 'chr' command