error with genome_homer.sh

[Kevinxsn]

Checks before submitting the issue

• [x] I installed the latest Dictys version successfully
• [x] I downloaded the whole folder for the tutorial
• [x] I ran the tutorial cells and notebooks (if more than one) in the correct order and only once
• [x] The preceeding cells and notebooks finished successfully (i.e. the reported error is the first encountered)

Describe the error

• How did you install Dictys (which option)? With Anaconda (option one)

• Which tutorial?

1-data.ipynb

• What (full message) and where (cell and notebook being executed) was the error? The cell under genome %%bash dictys_helper genome_homer.sh hg38 ../data/genome

By running the command, it told me that Error: reference genome hg38 not found in homer with some other error messages, the notebook files have been attached.

I ran Dictys several times a couple of months ago without any issues. However, when I tried running it yesterday, I encountered this error message.

• Did you deviate from any of the tutorial instructions? *No

Optional steps (may accelerate troubleshooting)

• Attach the error notebook and all preceeding notebooks with run output *https://drive.google.com/file/d/1vBDBOFsUptk-Boav2gb5ausFja7mK4zS/view?usp=sharing

[lingfeiwang]

Thanks for reporting the issue. Possibly you have installed multiple versions of hg38. You can check it inside your conda environment with:

cd "$(dirname "$(dirname "$(realpath "$(which homer)")")")"
./configureHomer.pl -list 2> /dev/null | grep hg38

What does this output? If you see multiple rows with different versions, can you remove all other versions and only keep the one you want to use?

[github-actions[bot]]

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