bpipe
bpipe copied to clipboard
ssadedin
Bpipe - a tool for running and managing bioinformatics pipelines
I'm using bpipe's `chr` statement to process bam files by chromosome. One of the stages in my pipeline produces two sets of bam files with names like `...bam` and `...bam`....
'multi' and 'multiExec' is a very useful way to parallelize the processing inside a bpipe stage. It would be great if the support of arbitrary cluster job configuration name can...
_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...
@ssadedin I use bpipe-0.9.9 tar ball, and have changed the file: 'templates/executor/sge-command.template.sh' :L2 from #\$ -wd ${bpipe.Runner.canonicalRunDirectory} to #\$ -cwd because the former one did not work correctly. And now...
I'd like to always run the checks regardless the condition of the previous $output, is this possible? It seems that the check class has a override option, but I don't...
Dear bpipe, I am running bpipe_0.9.9 on a Mac. When I launch a parallel bpipe script that copies 100 files, it works fine, until I include a `check` statement, and...
Hi, Is it possible to add support to pass parameters to bpipe.config? Something like you mentioned below: ``` commands { run_bwa { jobname = { "RUN_BWA_${SAMPLE_NAME}" } } } ```...
Hi All, I have a problem to test resuming capacity of Bpipe. Here is my code test3.pipe --- hello = { exec "echo Hello" exec "ls" exec "sleep 30" exec...
The "using" functionality is permanently broken if load is invoked in a stage. The following prints out "value is $value" instead of "value is goodbye": ``` loadme = { exec...
When calling bpipe -h a .bpipe directory still seems to be created. Im using a script to cycle through various installed applications to determine their versions and it fell over...
