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To continue discussion from #92
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Currently, the stdout of the cwl-runner is loaded into job.output by update_job in XenonRemoteFiles, then it gets overwritten by publish_job_output() in LocalFiles. But those are really different thin…
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As per request of @nielsdrost and @bpmweel we should think about serializability of the basic Xenon objects (to whatever format, it does not necessarily have to be java.io.Serializable but could also …
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Hi Brad,
We're experiencing a somewhat weird issue.
We run bcbio with iPython on a torque cluster, where the bcbio_nextgen.py command is run as a single core job, which then spawns the iPython job…
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## Description
As a developer, I would like Travis CI to run a battery of tests using the toy data for every commit and pull request, in order to ensure we don't break anything.
## Estimate
…
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While running the pipeline failed with the STAR error below. The pipeline was run on a AWS c4.8xlarge instance with 1 Terabyte of disk space on
root@4f374c77a227:/# lsb_release -a
No LSB modules ar…
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This can apply to both the website and the command line tool. It would be very nice to autogenerate a usage message, similar to what a lot of Linux tools do when you pass them a --help. This could b…
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## Bug Report
### Expected behaviour
Entering no parameters on all commands shows usage instructions
ex:
```
$ dockstore
____ _ _
| _ \ ___ ___| |…
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## Automated error report
### Description
Just when doing Magit-status, I get that error. It happens in other repos too. One common thing seems to be that `magithub-issue--process-line` chokes o…
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### Summary
When the crash occurred, I could copy some info from `Visual Studio`:
```
Unhandled exception at 0x00AC7691 in sublime_text.exe: 0xC000041D: An unhandled exception was encountered dur…