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cistrome / MIRA

Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
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"mira.tl.get_motif_hits_in_peaks" results in bin/sh 1:moods-dna.py not found when in environment #17

Closed Chadmiumoxid closed 1 year ago

Chadmiumoxid commented 1 year ago

So just as the title says I followed the tutorial until the step mira.tl.get_motif_hits_in_peaks and got an error telling me that moods-dna.py cannot be found, despite it being installed.

After trying for a long tim, I just copied the file from my work environment into my base environment and it suddenly worked. Now I am not sure whether the problem was my environment/python (always a possibility) or if the code in the package does not link to the correct folder. Just FYI and maybe it helps other people with the same problem.

Other than that MIRA works extremely well! Thanks a lot

AllenWLynch commented 1 year ago

Thank you for bringing up this issue. The Moods3 package for motif calling is the only C component of MIRA, so installation can be more complicated. Though I have not experienced any installation failures I will keep an eye out for them.

Do you remember if you installed with pip or conda? And which version of those tools you used?

AL

Chadmiumoxid commented 1 year ago

Hi Allen, sorry for the late answer, I thought I had written it already....

I used conda and conda-forge to install MIRA as suggested at https://mira-multiome.readthedocs.io/en/latest/index.html

When or how the Moods3 package was installed I have no idea, as it was probably a dependency that got installed without me noticing.