bpipe
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ssadedin
Bpipe - a tool for running and managing bioinformatics pipelines
_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...
Hi, I run into the following error while testing bpipe. $ echo $PATH /usr/local/apps/bpipe/0.9.9.2/bin:/usr/local/apps/parpipe/current/scripts:/usr/local/Anaconda/envs/py2.7/bin:/usr/local/bin:/usr/local/mysql/bin:/usr/X11R6/bin:/usr/local/jdk/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/bin:/usr/bin:/usr/X11R6/bin:/home/maoj/bin:/home/maoj/bin $pwd /usr/local/apps/bpipe/0.9.9.2/bin $ ./bpipe run ../helloworld.pipe java.lang.ClassNotFoundException: bpipe.Runner at org.codehaus.groovy.tools.RootLoader.findClass(RootLoader.java:179) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at org.codehaus.groovy.tools.RootLoader.loadClass(RootLoader.java:151) at java.lang.ClassLoader.loadClass(ClassLoader.java:357)...
I installed version 0.9.9.2 and added the bpipe-master/bin/ directory to my PATH. I was attempting to run the "hello world" test, and it fails: `$ bpipe helloworld.pipe java.lang.ClassNotFoundException: bpipe.Runner at...
Hi， I tried , def x = 26 def y = 10 def resultDiv = x.div(y) // or x / y but Bpipe can not support these codes from a...
HI, when I use bpipe to run my pipeline groovy , I find it will produce so many sub process(bpipe run) with java . my linux has installed SGE ....
Hi, The chromosome names of some genome assembly does not start with 'chr' as the prefix(e.g. human b37). So is that possible to add an additional argument to chr statement...
I ran a small number of subjects (6) on an sge cluster config in bpipe, I also have concurrency requirements set in the local pipeline (uses threads). The pipeline did...
I had a "stale" bpipe pipeline running from a control machine crash and when I went to restart the pipeline bpipe saw this and asked if I wanted to kill...
I'm encountering an issue with bpipe where a `from produce` block is executed twice. The pipeline stage looks something like this: ``` merge_bam = { def sample = input.split('/')[-1] sample...
Just noticed this at the end of a pipeline: ``` ======================================== Pipeline Succeeded ======================================== e_images /tmp/847724.1.all.q/tmp.5YBUIO0CyX/t.rgb 'black' -size 1920 397 /tmp/847724.1.all.q/ILT_4057_CUtJK/ILT_CqPvf.rgb 1603 11 /tmp/847724.1.all.q/ILT_4057_CUtJK/ILT_wFAiU.rgb 1282 11 /tmp/847724.1.all.q/ILT_4057_CUtJK/ILT_YdEeb.rgb 962 11 /tmp/847724.1.all.q/ILT_4057_CUtJK/ILT_a97jh.rgb...