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ssadedin
Bpipe - a tool for running and managing bioinformatics pipelines
Hi Simon, Every time I use a new feature of bpipe, I'm trying to put my experience into words to help you with documentation: Splitting input files using wildcards: run...
Here's my pipeline: ``` beastnormalize = { branch.origname = "$input" exec "beast_normalize $input.mnc $output.mnc $output.xfm -modeldir $TEMPLATE_DIR" } beastmask = { exec "mincbeast -clobber -verbose $LIBRARY_DIR $input.mnc $output.mnc -fill -median...
_From [[email protected]](https://code.google.com/u/101816960151431571338/) on 2014-10-11T08:13:56Z_ Using the "from" structure I can access outputs from previous stages in the pipeline, but I don't seem to be able to access the original input...
In https://code.google.com/p/bpipe/wiki/ParallelTasks the instructions discuss ordering and grouping with ""input_%_*.txt"", but there is never an explicit `Bpipe.run` statement, which explains how to use input splitting to run some pipeline components...
_From [[email protected]](https://code.google.com/u/101816960151431571338/) on 2014-10-12T05:19:17Z_ What steps will reproduce the problem? 1. Run pipeline with bpipe -r mypipeline 2. Open doc/index.html What is the expected output? What do you see instead?...
My environment is Groovy Version: 2.3.7 JVM: 1.7.0_71 Vendor: Oracle Corporation OS: Mac OS X When I try to run bpipe tests, I get "VerifyError: Bad method call from inside...
Finding the output for a single command in complex pipeline can be extremely difficult. It would be very useful to have a way to see output for each command separately.
_From [[email protected]](https://code.google.com/u/101816960151431571338/) on 2014-10-11T16:12:00Z_ What steps will reproduce the problem? 1. start a bpipe job (bpipe run -d output mincbeast.pipe input/*.mnc) with executor="sge" 2. Ctrl-C and allow job to continue...
_From [[email protected]](https://code.google.com/u/108158877086763603590/) on 2014-08-22T03:17:12Z_ The long-form options for '-r' and '-R' are both '--report'. '-r' takes no arguments (uses default template), '-R' takes 1 argument. The '--report' options goes with...
_From [[email protected]](https://code.google.com/u/106823827442770052555/) on 2014-07-16T14:57:01Z_ I have a pipeline that runs steps in parallel. The pipeline works very nicely, however the report is not consistent with what has been run. Here...