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nasa / GeneLab_Data_Processing

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Files Not available from source #8

Closed skr3178 closed 2 years ago

skr3178 commented 2 years ago

image

When I run this code link

https://github.com/nasa/GeneLab_Data_Processing/tree/27e0607f6abd2c58669ba399a19b774f06243124/RNAseq/GLDS_Processing_Scripts/GLDS-379/GLDS_version_3/ERCC_Analysis

there are some errors. The json files don't appear to be available. Thanks in advance

asaravia-butler commented 2 years ago

Those processing scripts retrieved the ISA archive file using an api endpoint that has since been retired.

The call to that retired api endpoint has been replaced in the current processing protocol with directly supplying the local ISA archive path:

https://github.com/nasa/GeneLab_Data_Processing/blob/master/RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-F.md#10a-evaluate-ercc-count-data-in-python

The ISA archive can be retrieved using one of the following options:

  1. Download using the GeneLab website interface: https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-379
  2. Download using the GeneLab public API: https://genelab.nasa.gov/genelabAPIs
skr3178 commented 2 years ago

Thank you