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## System and Software
* aicsimageio Version: 4.11.0
* Python Version: 3.11.4
* Operating System: mac os 13.3
## Description
I am trying to access the ome_metadata of a czi file.
I.e. I am d…
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### Feature Description
Either in the cookiecutter or somewhere visible we'll need to make sure that plug-ins specify which file formats they support. Specifically they will need to mention whi…
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When I run the program with the simplest params
```
$ ./kmers -p ~/github/my/rase-db-spneumoniae-sparc/isolates/28PCJ.fa -k31
```
I get
```
CatactttcctctttaTattgtattgataccaActtgtttgtagacttTtc…
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**If you know what is happening, here is the link to vote: https://rankedchoices.com/AICSImageNaming**
If you don't know what is happening, read below.
---
Hello everyone I have pinged and to…
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When I install cwltoil after cwl-runner and cwltool , cwl-runner does not run correctly.
I test with this example
[Common Workflow Language User Guide: Essential Input Parameters](http://www.commo…
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## Description
Current `channel_axis` implementation assumes to have the same binning for all channels to `np.stack` before returning. But it fails in most real cases, apparently. This issue was …
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Hi all
I am attempting to liftover annotations for my assembly hub, but it seems that the halLiftover job is adding an unknown option `--outBedVersion`. I see that the command called by the job is …
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Dear all,
I am attempting to use `hal2assemblyHub.py` so that I can perform a synteny analysis of the aligned genomes of the species I am working with. I have encountered an error, pasted below, th…
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Hello,
I am running the command:
hal2mafMP.py alignment.hal alignment.maf --refGenome Jc --numProc 10
I am getting the error:
Traceback (most recent call last):
File "/c1/apps/cactus/1.2.…
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Getting the following error running on grid engine.Running the example cwl workflow in documentation. https://toil.readthedocs.io/en/latest/gettingStarted/quickStart.html#cwlquickstart
Using toil ver…