Jason L Weirather

Working directory path with space and parentheses

5

I have an similar issue to this [https://github.com/broadinstitute/cromwell/issues/1306](https://github.com/broadinstitute/cromwell/issues/1306), but I don't think OP's solution fits whats going in my case since input files are not part of the issue. Using...

Docker is missing dependencies for 16S workflow

3

Trying to execute the 16s workflow via docker. From the documentation it sounded like only `usearch` would be missing due to its licensing issues, however it seems that `vsearch` is...

Error installing on Mac OS

6

I ran into a problem trying to install facets on what as far as I know is a pretty normal environment of R 3.4.0 on MacOS. ``` > devtools::install_github("mskcc/facets", build_vignettes...

The error rate/pattern calculations are supposed to be based on random selections of reads, so the expected behavior of the software would be that if you ran it more than...

strelka is not well a tested

1

It doesn't look like strelka is covered in the test cases included with polysolver. we don't have any current errors in it, but it was not a straitforward build since...

We should make temporary directory something that can be set when run

you have to make the output directory before running the command.

Fix for hanging when run in an off-line environment

2

Proposed fix for the issue where running in an off-line environment hangs on check_for_updates. Adds a default 10 second timeout to the request Shortened to 3 second timeout in the...

Containerized execution hangs because of update checks

5

**Describe the bug** While executing comfy-cli in a docker container, execution hangs when the code calls `comfy_cli.update`'s `check_for_updates` function. **To Reproduce** 1. Install comfy-cli in a docker container 2. Disable...