Add setup script and updates for wilms data #818
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This looks good overall, but I think you accidentally deleted a line in the sync script and you shouldn't need one you added.
I also suggested updating the environment variable name to better match conventions, and to support using the currently active profile more easily. We could make the same updates to the Ewings script, or just leave everything as is...
scripts/syncup-s3.sh
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| @@ -37,14 +37,14 @@ sync_dirs=( | |||
| scRNA-seq/data/tabula-muris/alevin-quant/10X_P7_12 | |||
| scRNA-seq/data/reference | |||
| scRNA-seq/index/Mus_musculus | |||
| scRNA-seq-advanced/data/ewing-sarcoma/processed | |||
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I don't think you meant to remove this?
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Copy/paste gone wrong indeed!
scripts/syncup-s3.sh
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| @@ -63,6 +63,7 @@ sync_files=( | |||
| scRNA-seq-advanced/data/ewing-sarcoma/annotations/ewing_sarcoma_sample_metadata.tsv | |||
| scRNA-seq-advanced/data/rms/annotations/rms_sample_metadata.tsv | |||
| scRNA-seq-advanced/data/reference/hs_mitochondrial_genes.tsv | |||
| scRNA-seq-advanced/data/wilms-tumor/processed/SCPCS000203/SCPCL000240_processed.rds | |||
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We should not need to include the individual file here. The only time this is needed is if we don't want to upload the entire folder. Nothing nested in a directory above should be needed here.
scRNA-seq-advanced/setup/wilms-tumor/download-openscpca-data.sh
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scRNA-seq-advanced/setup/wilms-tumor/download-openscpca-data.sh
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Closes #815
Closes #816
This PR adds a download script, and makes other relevant script modifications, for the Wilms tumor (SCPCP000006) sample we are going to be using for the scRNA-seq-advanced cluster evaluation exercise. I largely followed the approach from #807 to use OpenScPCA for download assistance. The single file downloaded is saved in
scRNA-seq-advanced/data/wilms-tumor/processed/SCPCS000203/SCPCL000240_processed.rds.While I was here, I also fixed the typo as noted in #816.