Download

  1. Title Binary Release Candidate for 0.9.8.6
  2. Release 0.9.8.6_rc
  3. Link bpipe-0.9.8.6_rc.tar.gz


  4. =========== 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