bpipe
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ssadedin
Bpipe - a tool for running and managing bioinformatics pipelines
I've read through several parts of the documentation and tutorial, but couldn't find a description of how dependencies are handled. If an input file is changed, does bpipe rerun that...
Sometimes I want to re-run an interrupted pipeline but I'm not sure exactly how I invoked it. If commandlog.txt contained that in the header it would be useful. ``` #bpipe...
Just putting this here to track the transition to template-based job submission and for testing/feedback - [X] SGE - complete in sge_fixes - [ ] torque/PBS - [ ] slurm...
See https://github.com/ssadedin/bpipe/pull/118 for discussion
I'm using LSF, several of my `bsub` jobs require variable parameters that can be a result of a previous step (e.g the number of nodes `-J jobName[1-$JOBS]`). It would be...
Hi there, Just wondering if you have any plans to support CWL (common workflow language) in bpipe? https://github.com/common-workflow-language/common-workflow-language Regards Dave
Not sure what it's for, but since it can't auto-install (based on reading build file), some install instructions are needed
Hi, sorry, pbspro issues again ;) The following line should be added to the wrapper: # PBS -V This will automatically export environment variables. Otherwise, one would have to always...
Some supercomputing clusters don't assign you a "SLOT" in the cluster aka a cpu, instead they assign you a whole computer with N CPUS. When this happens, it would be...
Hi, in development environment if I launch: ``` ./gradlew test -i ``` I notice that tests are not executed: ``` Skipping task ':compileTestGroovy' as it has no source files. ```...
