config: update phylop and phastcons conservation scores to 470 way

opencb · Dec 28, 2023 · f85a5c6 · f85a5c6
1 parent 79726a0
commit f85a5c6
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Showing 2 changed files with 8 additions and 7 deletions.
diff --git a/cellbase-core/src/main/resources/configuration.yml b/cellbase-core/src/main/resources/configuration.yml
@@ -109,9 +109,10 @@ download:
     host: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/release_notes.txt
   conservation:
     host: https://hgdownload.cse.ucsc.edu/goldenPath/
+    version: "2022-08-30"
   gerp:
     host: http://ftp.ensembl.org/pub/release-110/compara/conservation_scores/91_mammals.gerp_conservation_score/gerp_conservation_scores.homo_sapiens.GRCh38.bw
-    version: "2023-04-22"
+    version: "2023-05-17"
   clinvar:
 #    host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2021-07.xml.gz
 #    host: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2022-02.xml.gz

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/download/GenomeDownloadManager.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/download/GenomeDownloadManager.java
@@ -115,16 +115,16 @@ public List<DownloadFile> downloadConservation() throws IOException, Interrupted
                 List<String> phastconsUrls = new ArrayList<>(chromosomes.length);
                 List<String> phyloPUrls = new ArrayList<>(chromosomes.length);
                 for (String chromosome : chromosomes) {
-                    String phastConsUrl = url + "/phastCons100way/hg38.100way.phastCons/chr" + chromosome
-                            + ".phastCons100way.wigFix.gz";
+                    String phastConsUrl = url + "/phastCons470way/hg38.470way.phastCons/chr" + chromosome
+                            + ".phastCons470way.wigFix.gz";
                     downloadFiles.add(downloadFile(phastConsUrl, conservationFolder.resolve("phastCons")
-                            .resolve("chr" + chromosome + ".phastCons100way.wigFix.gz").toString()));
+                            .resolve("chr" + chromosome + ".phastCons470way.wigFix.gz").toString()));
                     phastconsUrls.add(phastConsUrl);
 
-                    String phyloPUrl = url + "/phyloP100way/hg38.100way.phyloP100way/chr" + chromosome
-                            + ".phyloP100way.wigFix.gz";
+                    String phyloPUrl = url + "/phyloP470way/hg38.470way.phyloP470way/chr" + chromosome
+                            + ".phyloP470way.wigFix.gz";
                     downloadFiles.add(downloadFile(phyloPUrl, conservationFolder.resolve("phylop")
-                            .resolve("chr" + chromosome + ".phyloP100way.wigFix.gz").toString()));
+                            .resolve("chr" + chromosome + ".phyloP470way.wigFix.gz").toString()));
                     phyloPUrls.add(phyloPUrl);
                 }
                 String gerpUrl = configuration.getDownload().getGerp().getHost();