- remove -t multithreaded option due to bug pcingola/SnpEff#157

- restore snpeff uploader for clinvar
biothings · Feb 11, 2020 · fcf9584 · fcf9584
1 parent c835714
commit fcf9584
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diff --git a/src/hub/dataload/sources/clinvar/clinvar_upload.py b/src/hub/dataload/sources/clinvar/clinvar_upload.py
@@ -1,5 +1,4 @@
 from .clinvar_xml_parser import load_data as load_common
-import biothings.hub.dataload.uploader as uploader
 from hub.dataload.uploader import SnpeffPostUpdateUploader
 
 

diff --git a/src/hub/dataload/uploader.py b/src/hub/dataload/uploader.py
@@ -38,7 +38,7 @@ def do_snpeff(self, batch_size=SNPEFF_BATCH_SIZE, force=False, force_use_cache=F
         assert snpeff_doc, "No snpeff information found, has it been dumped & uploaded ?"
         snpeff_dir = snpeff_doc["download"]["data_folder"]
         # -q: when there's an update, there's a message on stderr....
-        cmd = "java -Xmx4g -jar %s/snpEff/snpEff.jar -t -noStats -noExpandIUB %s" % (snpeff_dir,version)
+        cmd = "java -Xmx4g -jar %s/snpEff/snpEff.jar -noStats -noExpandIUB %s" % (snpeff_dir,version)
         # genome files are in "data_folder"/../data
         genomes = glob.glob(os.path.join(snpeff_dir,"%s_genome.*" % version))
         assert len(genomes) == 1, "Expected only one genome files for '%s', got: %s" % (version,genomes)