1. Title bpipe-
  2. Release
  3. Link bpipe-

  4. # Bpipe Version
    ##  Summary
    Bpipe 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.
    ## Highlights
    ### Enhancements
     * Support for preallocated resources for commands and allocated compute resources that 
       persist between pipeline invocations. See the [documentation](
       for more details.
     * Support for using Groovy Grab/Grape to add libraries to pipeline
       (see [documentation](
     * 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