lib: fix Docker version
@@ -47,7 +47,7 @@ public class GeneDownloadManager extends DownloadManager {
private static final String GO_ANNOTATION_NAME = "EBI Gene Ontology Annotation";
private static final String DGIDB_NAME = "DGIdb";
private static final String GNOMAD_NAME = "gnomAD";
- private static final String DOCKER_IMAGE = "opencb/cellbase-builder:5.0.0-SNAPSHOT";
+ private static String DOCKER_IMAGE;
private static final Map<String, String> GENE_UNIPROT_XREF_FILES;
@@ -64,6 +64,8 @@ public class GeneDownloadManager extends DownloadManager {
public GeneDownloadManager(String species, String assembly, Path targetDirectory, CellBaseConfiguration configuration)
throws IOException, CellbaseException {
super(species, assembly, targetDirectory, configuration);
+
+ DOCKER_IMAGE = "opencb/cellbase-builder:" + configuration.getApiVersion();
}
public GeneDownloadManager(CellBaseConfiguration configuration, Path targetDirectory, SpeciesConfiguration speciesConfiguration,
@@ -72,7 +74,8 @@ public class GeneDownloadManager extends DownloadManager {
}
- public List<DownloadFile> downloadEnsemblGene() throws IOException, InterruptedException {
+ @Override
+ public List<DownloadFile> download() throws IOException, InterruptedException {
logger.info("Downloading gene information ...");
Path geneFolder = downloadFolder.resolve("gene");
Files.createDirectories(geneFolder);
@@ -237,15 +240,11 @@ public class GeneDownloadManager extends DownloadManager {
return downloadFiles;
}
- private void runGeneExtraInfo(Path geneFolder) throws IOException, InterruptedException {
+ private void runGeneExtraInfo(Path geneFolder) throws IOException {
logger.info("Downloading gene extra info ...");
AbstractMap.SimpleEntry<String, String> outputBinding = new AbstractMap.SimpleEntry(geneFolder.toAbsolutePath().toString(),
"/ensembl-data");
-
- Map<String, String> dockerParams = new HashMap<>();
- dockerParams.put("it", "");
-
String ensemblScriptParams = "/opt/cellbase/gene_extra_info.pl --verbose --outdir /ensembl-data";
try {
