# 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