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AllenInstitute / scrattch.taxonomy

Allen Institute Taxonomy building R package
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added the capability to specify a log file path #25

Closed zrlewis closed 3 months ago

zrlewis commented 3 months ago

When calling loadTaxonomy using a h5ad file located in an S3 bucket, the following error occurs because it tries to write to the directory where the taxonomy is located:

> AIT.anndata = loadTaxonomy(taxonomyDir = '../data/taxonomies/Taxonomies/AIT21.0_mouse', anndata_file="HANN.AIT21.0.h5ad")
[1] "Loading reference taxonomy into memory from .h5ad"
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/data/taxonomies/Taxonomies/AIT21.0_mouse/checkTaxonomy_log.txt': Read-only file system

This PR is to allow a user to specify a log file location that differs from the taxonomy file location.

UCDNJJ commented 3 months ago

@inkarkapen Please bump the version of scrattch.taxonomy and rebuild the current docker with @zrlewis's update.