fix for broken URLs on stanford mitra

kundajelab · Jan 3, 2019 · 562c8ed · 562c8ed
1 parent c44dcbf
commit 562c8ed
Showing 1 changed file with 32 additions and 32 deletions.
diff --git a/install_genome_data.sh b/install_genome_data.sh
@@ -40,59 +40,59 @@ echo
 if [[ $GENOME == "hg19" ]]; then
 
   REF_FA="http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/referenceSequences/male.hg19.fa.gz"
-  # UMAP="http://mitra.stanford.edu/kundaje/genome_data/hg19/globalmap_k20tok54.tgz"
+  # UMAP="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/globalmap_k20tok54.tgz"
   BLACKLIST="http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz"
 
   # data for ATAQC
-  TSS_ENRICH="http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/hg19_gencode_tss_unique.bed.gz"
-  DNASE="http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz"
-  PROM="http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/reg2map_honeybadger2_dnase_prom_p2.bed.gz"
-  ENH="http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/reg2map_honeybadger2_dnase_enh_p2.bed.gz"
-  REG2MAP="http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/dnase_avgs_reg2map_p10_merged_named.pvals.gz"
-  ROADMAP_META="http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/eid_to_mnemonic.txt"
+  TSS_ENRICH="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/ataqc/hg19_gencode_tss_unique.bed.gz"
+  DNASE="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz"
+  PROM="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/ataqc/reg2map_honeybadger2_dnase_prom_p2.bed.gz"
+  ENH="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/ataqc/reg2map_honeybadger2_dnase_enh_p2.bed.gz"
+  REG2MAP="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/ataqc/dnase_avgs_reg2map_p10_merged_named.pvals.gz"
+  ROADMAP_META="https://storage.googleapis.com/encode-pipeline-genome-data/hg19/ataqc/eid_to_mnemonic.txt"
 
 elif [[ $GENOME == "mm9" ]]; then
 
   REF_FA="http://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/mm9.2bit"
-  # UMAP="http://mitra.stanford.edu/kundaje/genome_data/mm9/globalmap_k20tok54.tgz"
-  BLACKLIST="http://mitra.stanford.edu/kundaje/genome_data/mm9/mm9-blacklist.bed.gz"
+  # UMAP="https://storage.googleapis.com/encode-pipeline-genome-data/mm9/globalmap_k20tok54.tgz"
+  BLACKLIST="https://storage.googleapis.com/encode-pipeline-genome-data/mm9/mm9-blacklist.bed.gz"
 
   # data for ATAQC
-  TSS_ENRICH="http://mitra.stanford.edu/kundaje/genome_data/mm9/ataqc/mm9_gencode_tss_unique.bed.gz"
-  DNASE="http://mitra.stanford.edu/kundaje/genome_data/mm9/ataqc/mm9_univ_dhs_ucsc.from_mm10.bed.gz"
-  PROM="http://mitra.stanford.edu/kundaje/genome_data/mm9/ataqc/tss_mm9_master.from_mm10.bed.gz"
-  ENH="http://mitra.stanford.edu/kundaje/genome_data/mm9/ataqc/mm9_enh_dhs_ucsc.from_mm10.bed.gz"
-  REG2MAP_BED="http://mitra.stanford.edu/kundaje/genome_data/mm9/ataqc/mm9_dhs_universal_ucsc_v1.bed.gz"
-  REG2MAP="http://mitra.stanford.edu/kundaje/genome_data/mm9/ataqc/dnase_avgs_merged_named.fseq.vals.gz"
-  ROADMAP_META="http://mitra.stanford.edu/kundaje/genome_data/mm9/ataqc/accession_to_name.txt"
+  TSS_ENRICH="https://storage.googleapis.com/encode-pipeline-genome-data/mm9/ataqc/mm9_gencode_tss_unique.bed.gz"
+  DNASE="https://storage.googleapis.com/encode-pipeline-genome-data/mm9/ataqc/mm9_univ_dhs_ucsc.from_mm10.bed.gz"
+  PROM="https://storage.googleapis.com/encode-pipeline-genome-data/mm9/ataqc/tss_mm9_master.from_mm10.bed.gz"
+  ENH="https://storage.googleapis.com/encode-pipeline-genome-data/mm9/ataqc/mm9_enh_dhs_ucsc.from_mm10.bed.gz"
+  REG2MAP_BED="https://storage.googleapis.com/encode-pipeline-genome-data/mm9/ataqc/mm9_dhs_universal_ucsc_v1.bed.gz"
+  REG2MAP="https://storage.googleapis.com/encode-pipeline-genome-data/mm9/ataqc/dnase_avgs_merged_named.fseq.vals.gz"
+  ROADMAP_META="https://storage.googleapis.com/encode-pipeline-genome-data/mm9/ataqc/accession_to_name.txt"
 
 elif [[ $GENOME == "hg38" ]]; then
 
   REF_FA="https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.gz"
-  BLACKLIST="http://mitra.stanford.edu/kundaje/genome_data/hg38/hg38.blacklist.bed.gz"
+  BLACKLIST="https://storage.googleapis.com/encode-pipeline-genome-data/hg38/hg38.blacklist.bed.gz"
 
   # data for ATAQC
-  TSS_ENRICH="http://mitra.stanford.edu/kundaje/genome_data/hg38/ataqc/hg38_gencode_tss_unique.bed.gz"
-  DNASE="http://mitra.stanford.edu/kundaje/genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.hg19_to_hg38.bed.gz"
-  PROM="http://mitra.stanford.edu/kundaje/genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_prom_p2.hg19_to_hg38.bed.gz"
-  ENH="http://mitra.stanford.edu/kundaje/genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_enh_p2.hg19_to_hg38.bed.gz"
-  REG2MAP_BED="http://mitra.stanford.edu/kundaje/genome_data/hg38/ataqc/hg38_celltype_compare_subsample.bed.gz"
-  REG2MAP="http://mitra.stanford.edu/kundaje/genome_data/hg38/ataqc/hg38_dnase_avg_fseq_signal_formatted.txt.gz"
-  ROADMAP_META="http://mitra.stanford.edu/kundaje/genome_data/hg38/ataqc/hg38_dnase_avg_fseq_signal_metadata.txt"
+  TSS_ENRICH="https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_gencode_tss_unique.bed.gz"
+  DNASE="https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.hg19_to_hg38.bed.gz"
+  PROM="https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/reg2map_honeybadger2_dnase_prom_p2.hg19_to_hg38.bed.gz"
+  ENH="https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/reg2map_honeybadger2_dnase_enh_p2.hg19_to_hg38.bed.gz"
+  REG2MAP_BED="https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_celltype_compare_subsample.bed.gz"
+  REG2MAP="https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_dnase_avg_fseq_signal_formatted.txt.gz"
+  ROADMAP_META="https://storage.googleapis.com/encode-pipeline-genome-data/hg38/ataqc/hg38_dnase_avg_fseq_signal_metadata.txt"
 
 elif [[ $GENOME == "mm10" ]]; then
 
   REF_FA="https://www.encodeproject.org/files/mm10_no_alt_analysis_set_ENCODE/@@download/mm10_no_alt_analysis_set_ENCODE.fasta.gz"
-  BLACKLIST="http://mitra.stanford.edu/kundaje/genome_data/mm10/mm10.blacklist.bed.gz"
+  BLACKLIST="https://storage.googleapis.com/encode-pipeline-genome-data/mm10/mm10.blacklist.bed.gz"
 
   # data for ATAQC
-  TSS_ENRICH="http://mitra.stanford.edu/kundaje/genome_data/mm10/ataqc/mm10_gencode_tss_unique.bed.gz"
-  DNASE="http://mitra.stanford.edu/kundaje/genome_data/mm10/ataqc/mm10_univ_dhs_ucsc.bed.gz"
-  PROM="http://mitra.stanford.edu/kundaje/genome_data/mm10/ataqc/tss_mm10_master.bed.gz"
-  ENH="http://mitra.stanford.edu/kundaje/genome_data/mm10/ataqc/mm10_enh_dhs_ucsc.bed.gz"
-  REG2MAP_BED="http://mitra.stanford.edu/kundaje/genome_data/mm10/ataqc/mm10_celltype_compare_subsample.bed.gz"
-  REG2MAP="http://mitra.stanford.edu/kundaje/genome_data/mm10/ataqc/mm10_dnase_avg_fseq_signal_formatted.txt.gz"
-  ROADMAP_META="http://mitra.stanford.edu/kundaje/genome_data/mm10/ataqc/mm10_dnase_avg_fseq_signal_metadata.txt"
+  TSS_ENRICH="https://storage.googleapis.com/encode-pipeline-genome-data/mm10/ataqc/mm10_gencode_tss_unique.bed.gz"
+  DNASE="https://storage.googleapis.com/encode-pipeline-genome-data/mm10/ataqc/mm10_univ_dhs_ucsc.bed.gz"
+  PROM="https://storage.googleapis.com/encode-pipeline-genome-data/mm10/ataqc/tss_mm10_master.bed.gz"
+  ENH="https://storage.googleapis.com/encode-pipeline-genome-data/mm10/ataqc/mm10_enh_dhs_ucsc.bed.gz"
+  REG2MAP_BED="https://storage.googleapis.com/encode-pipeline-genome-data/mm10/ataqc/mm10_celltype_compare_subsample.bed.gz"
+  REG2MAP="https://storage.googleapis.com/encode-pipeline-genome-data/mm10/ataqc/mm10_dnase_avg_fseq_signal_formatted.txt.gz"
+  ROADMAP_META="https://storage.googleapis.com/encode-pipeline-genome-data/mm10/ataqc/mm10_dnase_avg_fseq_signal_metadata.txt"
 
 elif [[ $GENOME == "saccer3" ]]; then