ReleaseNotes.txt

=========== Changes for Bpipe Version 0.9.8.6.cgp3.0.4 ============

		- Raised LSF query time to 1min in ForwardHost.groovy, changed version 

=========== Changes for Bpipe Version 0.9.8.6.cgp3.0.3 ============

		- Raised LSF query time to 1min in ForwardHost.groovy

=========== Changes for Bpipe Version 0.9.8.6.cgp3.0.2 ============

		- Updated if condition when all the jobs have status exit

=========== Changes for Bpipe Version 0.9.8.6.cgp3.0.1 ============

		- Added -XX:+UseSerialGC - serial garbage collector

=========== Changes for Bpipe Version 0.9.8.6.cgp3 ============

		- removed break statement in LSF run condition

=========== Changes for Bpipe Version 0.9.8.6.cgp2 ============

		- removed explicit file.close as it doesn't exists in groovy :-)			

=========== Changes for Bpipe Version 0.9.8.6.cgp1 ============

		- updated lsf sub with conditions

		- lsf bsub checking time changed to 5sec -

		- All file handlers closed in Forwarder.groovy

		- added LSBjobindex as postfix parameter to err file name

=========== Changes for Bpipe Version 0.9.8.6 ============

   - fix: errors may printed about files not existing when attempting 
     to move to trash
   
   - fix bpipe jobs not printing jobs after user ctrl-c's out of 
     run command

   - fix incorrect default for procs_mode variable for torque 

   - fix ugly stack trace error when transform called without arguments 

   - fix failing to escape trailing . in split patterns 
    
   - branch.dir now ha a default value so that it is easier to put in reusable
     pipeline stages 
    
   - Ensure walltime gets interpreted as
     integer even if passed as String / BigDecimal / Long etc 
    
   - fix trash option not working in bpipe cleanup 
    
   - Fix default output directory not applied to second
     produce argument if first specifies a directory 
    
   - fix produce() with reference only to output.dir causing
     retry test to incorrectly indicate commands would run again
    
   - Fix incorrect file reported for errors when multiple
     external files loaded, added some comments, removed hard
     tabs 
    
   - fix branch variable not overriding default value of
     variable specified with var 
    
   - Fix files not checked after 'produce' if previously output and then 
     removed outside of bpipe 
    
   - Fix files not checked after 'produce' if
     previously output and then removed outside of bpipe 
    
   - fix 'inputs' variable with double file extension not always resolving
     only files matching both extensions     

   - fix output() function causing spurious errors about incompatible inputs 
     when combined with output variable extensions 
    
   - fix command not running when explicitly specified by produce() if another
     implicit output referenced by command 
    
   - Support for produce using wildcard based on regex (via ~) 
    
   - Add information about total run time to report and command log 

   - support to specify branch filter on command line, to limit
     running to a specific branch (for testing, usually) 
    
   - fix explicit output() combined with produce(...) resulting in
     inconsistent behavior 
    
   - Fix stack traces printed out when errors occur to use actual name of user 
     scripts instead of groovy generated ones 

   - fix build.gradle not working with existing gradle wrapper 
    
   - Implement default behavior for transform with
     more to() values than from() values instead of failing 

   - Fix output referenced inside check causing check to be
     skipped / behave incorrectly 

=========== Changes for Bpipe Version 0.9.8.6_rc2 ============

   - Issue 100: report does not accurately reflect repeated and
     parallel stages 
    
   - fix: inputs passed in wrong order to parallel stage after 'produce' when 
     lexical sorting differs to input order 
    
   - enhance: migrated all of Bpipe to use groovy 2.3.4 for JDK1.8 compatibility
    
   - Refactoring of basis for pipeline diagrams to solve longstanding bugs 
    
   - fix: commands not appearing in html report 
    
   - fix: bad log statement causing error if log
     file fails to appear, better behavior for distributed
     file systems where command may finish before output file becomes
     visible on remote node

   - fix: transform() from() to() form can result in Bpipe not detecting 
     command failure 
    
   - fix: pipeline fails if pipeline stage is referenced both with and without
     'using' 
    
   - fix: internal errors (eg: outofmemeory) possibly leaving the Pipeline in 
     corrupted internal state 
   
   - enhance: Make it possible to set custom R executable via
     bpipe.config 
    
   - fix: some status codes from PBS/torque occasionally causing errors in 
     logs 
    
   - fix: local commands don't show pid with bpipe status 
    
   - fix: status command showing old jobs and /
     or failing in situations where command objects are missing /
     corrupt 
    
   - enhance: add thread id to log file (debug)
    
   - fix: not all outputs from branches split by file pattern forwarded to
     downstream stage when number of files differs in each branch 
    
   - fix: take into account whole parent hierarchy in calculating
     total parallelism for computing variable 
    
   - enhance: support for sending proc_mode config param to custom executors and
     CUSTOM executor config attribute 
    
   - enhance: Torque/PBS: support for sending procs request using nodes/ppn attribute 
     instead of procs 
    
   - fix: 'forward' failing with cryptic errors when attempting to
     forward multiple files 
    
   - enhance: enabled matching of directory name in split pattern when
     directory present in pattern 

   - fix: second and later outputs possibly not cleaned up in some 
     situations of command failure 
    
   - fix: branch variables not accepted as required parameters 

   - fix: output does not include branch if no input as base and output 
     extension syntax used 
    
   - fix: R aborting when user hits control-c in some situations 
    
   - fix: some complex pipelines starting with list failing with errors 
    
   - fix: fixes for PBS Pro executor from Davide 
   
   - enhance: support for PBS Pro thanks to Davide Rambaldi 

=========== Changes for Bpipe Version 0.9.8.6_rc ============

   - support for 'load' to work with URLs for loading 
     scripts remotely

   - fix chr variable created by chr() not considered as satisfying 
     requires chr:...  
     
   - start and stop time not set by local command
     exector 
     
   - restrict use of auto filter to cases where chr actually 
     in operation 
     
   - file() construct sometimes returning paths with .. in them
     
   - Add pipeline stage name to printout in bpipe query 
     
   - support for multiple file extensions when using $output variable
     ($output.foo.bar.gz, etc) 
   
   - fix incorrect outputs resolved for filter when inputs are 
     resolved from a relative path leading with "." character 
     
   - fix preserve not resolving files specified by different absolute /
     relative paths to Bpipe's form, (thx Anthony)
     
   - Not serializable exception on legacy directories 
     
   - Remove legacy feature where output may
     be inferred from created files: does not behave reliably in
     parallelized pipelines 
     
   - support for multiple "preserve" patterns 

   - fix preserved status not displayed
     correctly by bpipe query 
     
   - support for grouping commands in tool database
     into 'modules' 
     
   - fix syntax errors in tool database 
     
   - added igv tools, fix GATK probe, add VEP to tools database 

   - fix binary report files copied as text causing corruption
     
   - add stage name to meta data properties saved for each
     output file 
    
   - fix filter sometimes expecting wrong input when
     file extension supplied 
     
   - fix "bpipe run" leaking a tail process each time on OSX 

   - support for generating reports using arbitrary groovy
     code in a separate script 
     
   - add tools and versions to meta data stored in 
     output properties 
     
   - fix status for SLURM displaying Torque in output 
     
   - fix possible conflicting output names on multiple branches 
     when nested branches cascade without intervening stages 

   - add support for referencing output graph in reports 
     
   - transform should be able to
     match whole file name, fix incorrect input can be resolved
     inside transform() to() construct 
    
   - display running time and pending output in response to 
     bpipe query 
   
   - Add procs to LSF executor 
     
   - refactored a lot of executor stuff to remove duplicated
     code, plus to allow for recording start of execution time
     separate to start of queuing time 

   - fix GB ignored as key for memory 

   - support to use ${output(...)} in commands instead of produce  

   - support for adding jars to classpath via bpipe.config 
     (libs="foo.jar:bar.jar...")

   - fix requires at pipeline stage level no longer working because 
     overriden by top level requires function 

   - experimental: multithread startup to ammeliorate long delays 
     when file system is slow

   - make it possible to remove the cwd option from lsf
     executor (see google group)

   - use -e instead of -eo for LSF since it is compatible with OpenLava 
     
   - ability to use multiple extensions for 'input' variable file 
     extensions, eg: $input.foo.bar.csv returns files ending in 
     '.foo.bar.csv'

   - fix input with file extension not requiring match on first 
     character in some cases 
     
   - fix problem in some weird cases where object has null class 
     
   - prevent errors when running in test mode with explicit 
     notifications sent in pipeline to 'file' channel
     
   - switch to SimpleTemplateEngine because GStringTemplateEngine is not
     observing classpath of added libraries, only core groovy
     libraries 
     
   - fix output directory set by command line
     resulting in inputs not correctly recognised in 2nd and
     later stages of pipeline 
     
   - fix required inputs using exact path instead of file name 
     
  
========== Changes for Bpipe Version 0.9.8.6_beta_3 ============

   - support for setting check message without failing or succeeding 
   - explicitly (check.message = "...." in otherwise clause) 

   - new check report to send / write a summary of all checks 
     as HTML (bpipe run -R checks ..., 
     send report('checks.html') ...)
    
   - documentation now available to reports based on user
     templates 

   - "utils" now provided to templates for generic
     utilities (escape, todo: documentation) 
     
   - Ensure full stack trace is
     logged in bpipe log when missing function encountered 
     
   - make produce() with directory use that directory rather 
     than coerce to default output dir 

   - added new supported commands to default help display 
     
   - fix parameters passed in by command line not resolvable in
     templates 

   - support 'send report(...) to file: <file name>'
     syntax 
     
   - fix subject line used incorrect in SMTP notifications
     
   - inputs not being correctly checked to be provided when specified 
     at root level 

   - don't display exception info when failure is due to
     value missing from specified inputs via 'inputs ...' statement
     
   - support for 'requires' at top level outside of pipeline 
     definition 
     
   - improve wording and display of error when required value is
     missing 

   - fix templates not able to see all classes available on
     classpath

   - removed all forms of throttling of R sessions (should now be
     unnecessary) as it can form a bottleneck in certain
     scenarios 


========== Changes for Bpipe Version 0.9.8.6_beta_2 ============

   - avoid warnings due to project properties (thanks Davide) 

   - refactored email functionality to use user configurable
     templates 

   - fix notifications for pipeline finished saying
     pipeline failed when it didn't 

   - support for displaying information about checks at end of pipeline 

   - more information in SMTP notifications, including checks 
     
   - Added option to override all checks for cases where there are 
     very many that have failed 
     
   - changed unknown communication provider to be a warning instead 
     of a pipeline terminating exception.

   - fix relative symbolic link to Bpipe not resolving properly 
     under Mac/OSX 

   - fix possibility of commands sometimes
     not being cleaned up (add pause before terminating Bpipe,
     after terminating child processes) 

   - Fix Slurm not returning failure exit code when
     job cancelled via bpipe stop (causing outputs not to be
     cleaned up)

   - Added "checks" command and "override" command to display and 
     override checks respectively

   - Fix transforms sometimes applying in such a way
     as to add branch name with no period separating them from
     the rest of the file name (regression)
     
   - fix transforms producing null outputs when no period in 
     input file name  (regression)
     
   - support for rendering pipeline diagrams as SVG 

   - support for specifying pipeline stages to ignore 
     in diagrams via noDiagram="..." in bpipe.config (annotations to 
     come in the future) 

   - fix diagrams generated incorrectly if 'segment'
     command used 

   - fix documentation failing to generate unless script has a
     relative or absolute path prefixing it 

   - some tweaks to avoid rare cases double
     dots appearing in file names with transform 

   - 'succeed' should terminate parent branch when all child
     branches terminated via succeed 

   - support for running a pipeline "until" a specified stage
     ( -u)  

   - support for send to use HTML templates instead of
     inline HTML 
     
   - support for 'succeed' and 'fail' to share
     'send' syntax to generate an email or IM along with the
     termination of the branch 

   - fix slurm executor sometimes
     treating slurm stdout and stderr temp files 
     as real outputs of pipeline 

   - Fix space inserted when withFlag used with flags 
     ending with "=" 
     
   - fix variables and functions loaded via 'load' not available until 
     pipeline launched (inside run { } ) 
     
   - allow global resource limits (as supported by -l flag 
     to bpipe) to be specified in bpipe.config as well 
   - 
   - support for sending emails and
     instant message notifications explicitly 
     from script, using syntax: send text 'hello' to gtalk, 
     and more advanced forms (documentation to come) 

   - support for using
     explicit regex pattern to split files to parallel 
     paths (as opposed to simplified pattern syntax) 
     just add ~ to pattern 
     
   - fix (very rare) possibility for duplicate file
     names when referencing 'inputs' 
     variable 
     
   - added support for matching numbers
     in input splitting patterns ('#') 

   - added support for gradle wrapper 
     
   - added gradle wrapper for easier building
     (now just use gradlew instead - of gradle, and it
     self downloads) 
     
   - fix custom resources not enforced when
     provided as map 

   - fix default build to autodetect Gridgain
     jars and compile without if not 
     found 

   - get mail.jar from Maven so default checkout compiles 
     
   - changes to allow "single" queue to handle
     multiple tasks (vlsci) 

   - fix 'bpipe status' displaying incorrect command for SLURM, PBS
     possibly others
     
========== Changes for Bpipe Version 0.9.8.6_beta_1 ============

   - fixed file(...) function sometimes returning file object
     for "<file>/." 

   - experimental feature: supply closure with ".using(...)" for lazy 
     evaluation, allowing reference to runtime pipeline variables in 
     configuration of pipeline stages

   - initial implementation of a 'bpipe status' command, to show exactly
     what is currently running 

   - Ability to explicitly cause a
     branch to either fail or succeed prematurely 
     (via "fail" and "succeed" commands) 

   - added support to transform a
     single file pattern to multiple targets 

   - ability to configure and customize reports from bpipe.config 
     (custom names, etc.), and to send by email when email notifications
     configured 

   - allow "procs" to be specified as integer in
     resource manager config 

   - fix first line of log file sometimes not showing when using 
     "bpipe log ..." 

   - "bpipe query" not working on files in non default output
      directories (eg: specified with output.dir=....) 

   - more graceful / better handling of errors
     that cause the script to not parse or load at all 

   - support for finding bpipe.config in the same directory as
     the pipeline script (which might be different to the
     directory that bpipe is running in) 

   - better handling of exception when probing tools in tool database 

   - new feature: allow for muliply by Map to set an explicit
     mapping of branch names to inputs 

   - special behavior for accompanies when dealing with 
     transforms: always adds
     extension to end of file rather than replacing 

   - allow requires to specify complete file name instead of just
     extension 

   - allow resolution of 'load' files relative to the pipeline
     script itself so that it is easy to maintain a pipeline
     file and ancillary files in the same directory 

========== Changes for Bpipe Version 0.9.8.5 ============

-   fix output.dir not working if transform annotation used 

-   fix silly mistake causing load external stages to fail 

-   fix loading a pipeline stage from within a loaded pipeline stage not
    working

-   added ability to set branch level variables that are carried forward
    through the pipeline via branch.<name> = "something" syntax

-   Fix output sometimes not fully flushed when running pipelines using
    resource managers

-   support for using arbitrary lists for parallelization over any  
    list of items

-   fix msg writing output during probes (causing double output in 
    certain situations)

-   when an output that is specified as an absolute / relative file that exists, 
    fix not seeing it in dependency graph

-   better file names when output extension occurs in combination with 
    introduction of branch name (foo.chr1.csv instead of foo.txt.chr1.csv)
    NOTE: in rare situations this might cause output file names to change,
    thus may cause outputs to get recomputed for existing pipelines (in rare cases)

-   allow command line region to override chr() within pipeline

-   fix command configuration sometimes not displaying name 

-   slightly better description of command for specifying report 
    template (see Google Group discussion)

-   fix R code failing when last line contains certain syntax

-   Enable specifying file name for reports (Patch from Ido Tamir,
    thank you!)

-   fix problems when multiple implicit outputs computed from same input file 
    (output1.foo and output2.foo end up the same file)

-   handle incorrect report template much more nicely than a giant stack
    trace

========== Changes for Bpipe Version 0.9.8.4.1 ============

-   fix middle parallel section causing spurious error if no inputs provided
    at start of pipeline

-   fix error when pipeline starts with parallel section and adds a
    subsequent stage (regression)

-   fix file splitting patterns not working properly for very specific case
    of a split wildcard (%) followed by 2 chars


========== Changes for Bpipe Version 0.9.8.4 ============

-    fix __bpipe_lazy_resource_threads__ appearing in
     output when commands fail instead of real value of $threads

-    fix __bpipe_lazy_resource_threads__ appearing in
     command log instead of real value of $thread

-    prevented tools being probed more often than needed

-    moved throttling of command execution into separate
     class, applied throttling to tool probing so as to lessen chances
     of exhausting threads or file handles when running with 
     large numbers of inputs and highly parallel pipelines

-    fix log.warn causing any UNKNOWN status code return
     from PBS/Torque to exit with error instead of retrying

-    fix filter transforms sometimes basing output file
     on wrong input 

-    preliminary SLURM support via Andrew Lonsdale (thanks!)

-    when a command is configured with to use a specific
     number of procs, that should override the magic $threads
     variable value

-    PBS / Torque support not sending memory config for
     queues other than 'batch' or 'smp'

-    hack: add ability to put extra classes into
     $BPIPE_LIB/extra-lib.jar for use in pipeline script

-    don't convert outputs containing paths to output
     folder

-    further support for inputs that are directories -
     prevent checking of timestamp of directory, search the 
     full output tree instead of just immediate inputs to stage 
     when a directory input is requested

-    fix glob outputs not recognized as already created
     when in explicitly set output folder

-    fix "using" construct causing diagrams to fail

-    fixed diagram failure on nested parallel section, and
     when a parallel section is the root element in the pipeline

-    fix diagrams failing with exception stack trace when
     pipeline is split by chromosome

-    fix diagrams not working when only a single stage
     defined in pipeline

-    add support for transform(".xml") to(".csv") { }
     style syntax (experimental)

-    better error message for referencing undefined function

-    fixed branch names including directory portions of
     input file paths when split on files from other directory

-    ensure variables can be overriden from the command
     line

-    show all commands when test mode aborts a multi
     command

-    option to show only output from single thread with
     bpipe log -t


========== Changes for Bpipe Version 0.9.8.3 ============


-    fix input not resolved by from / input ext when
     reference embedded in nested

-    fix %bin% expansion incorrect when tool command is
     part of the full path containing the tool itself - eg:
     /usr/local/bwa/bwa-0.5.9/bwa

-    fix possible double period in output file name (regression)

-    fix references to output.dir causing outputs to be
     inferred even when no outputs actually decided yet for
     stage (eg: before produce / transform / filter, etc.).

-    fix backslashes in file paths causing invalid output
     paths on Windows

-    fixed failures when files without extensions created
     as outputs / inputs

-    run commands using -e option with bash so that failure
     of any command within script results in abort

-    nicer error message when a filter encounters the
     situation that no inputs were provided

-    fix transform producing same output as input when
     output file of same type as input

-    add support for closure as value for variable default
     to compute default value at runtime, prevent referencing  
     unless actually needed (useful eg: if the default should be 
     an input when not provided)

-    attempt to fix out-of-order execution of pipelines
     that start with list and append stages after

-    support for "requires" to specify required parameters
     for a pipeline stage

-    support for multiple paths in BPIPE_LIB

-    support for script files in BPIPE_LIB (in addition
     to folders of scripts)

-    support for ordering of execution of modules in
     BPIPE_LIB

-    fix output files not merged correctly when multiple
     levels of nested
     parallel segments end at same point

-    updated to add withFlag for more stringent test case

-    changed build to use manually downloaded gridgain lib
     (GridGain pulled their repo support :-( )


========== Changes for Bpipe Version 0.9.8.1 ============

-  fix double spaced output

-  fix input.size() and inputs.size() throwing exceptions

-  fix potential incorrect output inferred in filter operation,
   causing 'expected output not found' error in some filter 
   scenarios

========== Changes for Bpipe Version 0.9.8.1 ============

-    Fix race condition causing occasional null pointer
     exception, making param_nested_parallel test fail

-    fix exception when using bpipe preserve

-    fix potential leading semicolon when executing command

-    fix for incorrect input inferred by filter if actual
     input used different to those supplied by previous stage

-    fixed regression causing '..' in filenames from output
     extension that operates like transform

-    fix double period in inferred output names when no
     explicit filter / transform present

-    fixed dependencies working incorrectly with produce; stage skipped even if
     actual inferred / used input was newer than actual inferred output

-    fix multiple instances of Bpipe running R scripts
     clashing other

-    support for "diagramOrientation="vertical" in
     bpipe.config to change orientation of diagrams

-    fix diagrams not generating correctly for some
     pipeline architectures

-    fix commands used to generate outputs sometimes
     displaying as "..." when using "bpipe query"

-    improvements to tool database - more links, better
     descriptions, etc.

-    to prevent some of the massive output 
     that comes from large pipelines when re-executing, buffer
     messages unless a stage actually does something.

-    support for producing custom reports, named by
     command line

-    added source for software schedule report

-    fix input ext on output with index referencing
     wrong output

-    fix cleanup not removing directory

-    fix glob on output folder not working

-    fixed output explicitly specified in produce() to be
     in folder still remapped to default output dir

-    added alternative bpipe runner that runs in background

-    fixed filterInputs still not working right with chr()
     behavior now defaults based on whether the input files contain
     chromosome references rather than always filtering


========== Changes for Bpipe Version 0.9.8 ============
 
-   fixed problems with quoted args becoming unquoted during launch
    (so eg: bpipe execute 'foo + bar' would not work)

-   fixed 'bpipe retry' not working with quoted arguments
    in commands

-   fixed filter sometimes incorrectly refusing to allow output files that
    should work basd on used inputs

-  fix $input1 not resolving in commands if there is only one input

-  fix no information about outputs printed when too many outputs

-  added 'withFlag' function on $inputs, $inputs.<ext> variables for easily
   adding multiple inputs with the same flag (eg: ${inputs.bam.withFlag("-I")})

-  strip leading spaces from commands when joining lines together for execution
   (prevent whitespace bloat in command log)

-  jobid now prepended in history file

-  support to retry specified job from history using
   bpipe retry <jobid>

-  prevent bpipe commands that fail with invalid
   arguments from getting logged in history

-  don't log full path to bpipe executable in history
   file (breaks if bpipe location / version changes)

-   fixed files failing to get cleaned up if same file was
    previously cleaned up + added warning if cleanup fails

-   fixed filter followed by from potentially resolving
    its own stage output as input

-   fix for mt issue around pipeline inputs (causing
    parallel_same_stage_outputs test to fail if you run
    it many times) - regression from beta 3/4

-   support for @intermediate and @accompanies
    (experimental) annotations

-   fixed failure to cleanup outputs that are inferred from output file
    extensions rather than transform / filter / produce when pipeline 
    stage fails

-   fixed multiple references to multiinput properties
    resulting in duplicated / missed outputs

-   fixed reference to inputs variable followed by
    reference to input variable returning wrong results

-   fixed later stages not resolving inputs from non-final
    stages in prior nested parallel segments

=========== Changes for Bpipe Version 0.9.8_beta_5 ============

-   more fixes to make config{} work properly
    fixed 'config' not working / failing to execute
    commands
-   fix parallel branches created from file pattern split
    not using split files as basis for outputs sometimes

=========== Changes for Bpipe Version 0.9.8_beta_4 ============

-   support for multiple split characters in input matching patterns

-   support for config closure to enable config across multiple commands or
    when using "multi"

-   slightly better messaging when skipping command due to existence, not
    based on time stamp

-   fix display of output to stderr when version probe command fails
    - send to log instead

-   experimental chaining of from and filter / transform

-   fix "from" causing original inputs not to be queried for files in some
    situations

-   fix "filter" nested in "from" failing to infer correct output when output 
    based on input other than input in "from" clause

-   fix possible exception when using $output.prefix

-   fixed second and later stages in nested parallel segments not always
    resolving correct inputs

-   fix attempts to use "split" in input variables failing (regression)

-   added support for use of "region" variable without genome or chr splitting
    to allow generic pipeline stages that can work with or without regions 
    specified
    
-   added command line option ("-L") to specify default value of region variable
    
-   fixed "from" to match multiple inputs if used in form from("*.txt") etc.

-   Added example for how to run paired end reads

-   fix output extension causing wrong / confusing behavior when incombination
    with a filter and unexpected input order

-   fix bpipe command leaving out eclipse folder from classpath

=========== Changes for Bpipe Version 0.9.8_beta_3 ============

-   Updated underlying groovy implementation to Groovy 2.1

-   Add "pre-existing" label to display of outputs that 
    weren't genereated by the current run

-   fix error when creating File objects from input /
    output

-   support for using numbered outputs with file extensions
    (eg: $output2.txt)

-   fixed outputs sometimes being recreated unnecessarily
    when multiple commands inside transform/filter

-   support for implicit 'thread' variable for auto
    allocating threads based on known concurrency

-   fixed duplicate output files for $output1,
    $output2,... if pipeline has no input files

-   fix jobs not always cleaned up from global job table

-   support for referencing a particular input with a
    particular extension using "$input<n>.<ext>"

-   fixed double period appearing in some file names when
    using filter

-   fixed order of output from "glob" depending on the
    vagaries of the file system or java internals by
    sorting it

-   made 'from' conform to the convention of multiple
    inputs of same time bumping to next actual input
    instead of returning the same over and over

=========== Changes for Bpipe Version 0.9.8_beta_2 ============

-   fixed multi not failing pipeline when an asynchronous
    command fails

-   making filter() conform to the same behavior as
    transform(): when a filter type is repeated, it moves
    to the next input (see google group discussion -
    https://groups.google.com/forum/?fromgroups=#!topic/bpipe-discuss/G58ExlG2Vgo

-   fixed error when reporting notification failures
    to user

-   fixed output extensions not working correctly with
    filter when multiple filters supplied

-   fix multi not actually parallelizing properly in
    some cases

-   fix regression in 'from' not accepting list (added
    test)

-   fixed from with multiple arguments ignoring first
    argument

-   fixed deadlock condition in using "multi" in certain
    cases

=========== Changes for Bpipe Version 0.9.8_beta_1 ============

-   More flexible model for concurrency management, enabling
    management of any kind of resource. Introduction of
    new keyword "uses" to declare resource usage for a block
    and command line options (-m, -l, -n) to control different
    aspects of concurrency

-   Complete re-implementation of dependency analysis so that
    Bpipe understands the depedency graph and can perform
    transitive dependency analysis to allow rerunning piplines
    without rebuilding unnecessary intermediate dependencies.
    (See Issue #2, http://code.google.com/p/bpipe/issues/detail?id=2)
    Includes support for new command line commands, 
    "bpipe query", "bpipe cleanup", and "bpipe preserve" to 
    display and manage dependencies, as well as annotations,
    "@preserved" to declare dependencies that should not be
    deleted in a "cleanup". 

-   support for new 'glob' function available within
    pipeline stages to facilitate pipelines that need to
    use wild card matches on input files.

-   Annotations can be used with lower case now. Upper case 
    still works, but some people feel @transform, @filter,
    etc. looks nicer.

-   Support for parallelizing by chromosome on existing
    files already split by chromosome. If your input files
    are split and named by chromosome, you can use 
    filterInputs parameter to make the existing
    files be used for inputs to the parallelization 
    eg. chr(1..2, filterInputs:true) 

-   Many various bug fixes and improvements to messaging,
    behaviour and output.