Download
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Title
Bpipe Binary Release 0.9.9.8
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Release
0.9.9.8
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Link
bpipe-0.9.9.8.tar.gz
=========== Changes for Bpipe Version 0.9.9.8 ============
- Feature: options statement for easy parsing of script specific
command line arguments
- Add workaround to fix possible failure on old pipelines checking
file existence
- BUG: Fix spurious error printed if broken symbolic link present
- BUG: prevent agent launched commands hanging due to if bpipe prompts
for information
- Feature: add fileSystemSyncTimeMs which allows for customizable delay in
file system sync before failing pipeline on missing output
- BUG: fix regression - transform using regex does not substitute groups
eg: transform('(.*)_R1.fastq') to("\$1.txt") { ... }
- Many fixes / optimisations to GCloud usage:
- make workingDirectory specified for stage automatically
placed within mounted storage
- inherit region from main config inside
filesystems, so it does not need to be double specified
- support preemptible flag passed to google cloud
instances
- add sha1 hash of pipeline path / host to
instanceid to make it unique b/w pipelines
- fix region configured
for cloud executor overriding region specified with -L
- search for root input files in all filesystems, not only
those configured as storages for stages
- fix zone flag missing from gcloud commands, don't
die mounting storage if instance not created
- support using split / partitioned regions in cloud provider storage
- BUG: Don't start executor pools when user is only testing the pipeline
- BUG: ensure that executors clean up even if they error in stop
command
- Fix table output format so it shows correctly in GitHub markdown
- Better behavior for bpipe test with send, and send for missing outputs
- BUG: input patterns with dir in the pattern causing error / exception
- Feature: support for reply -to in JMS bpipe agent
If the reply-to or JMSReplyTo header is set, the bpipe agent will now
send a message containing the original command and pipeline success / fail
to specified reply-to address (allows eg: camel inOut routing)
- BUG: Fix inverted logic causing incorrect detection of file existence
when file is out of sync, causing file systems with high latency
to fail sporadically
- Better tolerance of file system sync issues for files referenced
using file(...)
- BUG: `from` sometimes failing to ensure specified input is resolved in
preference to other available inputs preceding it in the
pipeline
- BUG: from sometimes selecting incorrect input in complex scenarios
- BUG: fix file system watchers still created even if poller watcher specified,
hence still resulting in file watcher exhaustion errors
- BUG: -d option not respected in some situations, incorrect output dir may
be used if default output already referenced
- Feature: Support for Groovy 2.5.6 via optional gradle.properties setting
- Feature: support for template dirs created by bpipe agent with incrementing
values. Directories containing {inc} will be named with auto-incrementing
counter.
- Feature: 'terminateOnError' flag in send attributes causes
notification failure as to be treated as error
- BUG: improve unfriendly / incorrect behavior when duplicate mappings exist in transform
- BUG: checks sometimes re-executing when not necessary
- Feature: `bpipe touch` command updates files from current run
of pipeline to new timestamps so they do not re-run on `bpipe run`.