lonsbio
lonsbio
The approach of replacing ambiguous (`N`) nucleotides in the barcode or UMI with a pseudorandom nucleotide was previously discussed in the context of `bustools correct` (https://github.com/BUStools/bustools/issues/12). At the time the...
When using the shebang support in `bpipe`, i.e. scripts leading with: ``` #!/usr/bin/env bpipe ``` the first output line to the terminal is always `Stripping shebang` ``` Stripping shebang ====================================================================================================...
_From [[email protected]](https://code.google.com/u/116548269372547513801/) on 2013-02-23T02:45:23Z_ What steps will reproduce the problem? 1. Download and unzip bpipe 2. Tried to run helloworld.pipe example from documentation (bpipe run helloworld.pipe) 3. get the error...
_From [[email protected]](https://code.google.com/u/106823827442770052555/) on 2012-10-21T11:47:01Z_ Sometimes certain operations are not completely reliable - whether just because the software is buggy, depends on unreliable network connections, hits transient resource starvation (eg. out...
_From [[email protected]](https://code.google.com/u/116481381496220708790/) on 2014-04-15T18:25:20Z_ Hi, switched our cluster to SGE the other day and wanted to run a simple bpipe pipeline. However, specifying resources as described in the documentation yields...
Use named pipes to fix sed and tail process not being killed on Max OS X 10.10
_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...
_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?...
_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...