fix: adjusting to GTEx upstream URL change (#71)

varfish-org · Dec 28, 2023 · b3ec6d8 · b3ec6d8
1 parent 307cf58
commit b3ec6d8
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Showing 8 changed files with 10 additions and 10 deletions.
diff --git a/download_urls.yml b/download_urls.yml
@@ -58,12 +58,12 @@
 - url: ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_GRCh37.tsv
 - url: ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_GRCh38.tsv
 
-- url: https://storage.googleapis.com/gtex_analysis_v8/annotations/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt
+- url: https://storage.cloud.google.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt
   excerpt_strategy:
     strategy: no-excerpt
     count: null
 
-- url: https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz
+- url: https://storage.cloud.google.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz
   excerpt_strategy:
     strategy: manual
     count: null

diff --git a/excerpt-data/2295c2a0487d0dab/url.txt b/excerpt-data/2295c2a0487d0dab/url.txt
diff --git a/...17-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz → ...17-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz b/...17-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz → ...17-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz
diff --git a/excerpt-data/95e8d788836873e9/url.txt b/excerpt-data/95e8d788836873e9/url.txt
diff --git a/excerpt-data/9e484a896c7516d6/url.txt b/excerpt-data/9e484a896c7516d6/url.txt
diff --git a/...sis_v8_Annotations_SampleAttributesDS.txt → ...sis_v8_Annotations_SampleAttributesDS.txt b/...sis_v8_Annotations_SampleAttributesDS.txt → ...sis_v8_Annotations_SampleAttributesDS.txt
diff --git a/excerpt-data/d0a5951ccb4cd824/url.txt b/excerpt-data/d0a5951ccb4cd824/url.txt
diff --git a/rules/work/genes/gtex.smk b/rules/work/genes/gtex.smk
@@ -34,11 +34,11 @@ rule genes_gtex_v8_download:  # -- download GTex v8 gene expression data
         r"""
         wget --no-check-certificate \
             -O {output.attributes} \
-            https://storage.googleapis.com/gtex_analysis_v8/annotations/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt
+            https://storage.cloud.google.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt
 
         wget --no-check-certificate \
             -O {output.genes_tpm} \
-            https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz
+            https://storage.cloud.google.com/adult-gtex/bulk-gex/v8/rna-seq/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz
 
         md5sum {output.attributes} > {output.attributes_md5}
         md5sum {output.genes_tpm} > {output.genes_tpm_md5}