fix(test): run search against ncbi nr

metagenomics · Jan 30, 2024 · 172fef4 · 172fef4
1 parent c7fe080
commit 172fef4
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Showing 2 changed files with 11 additions and 2 deletions.
diff --git a/bin/emgb.sh b/bin/emgb.sh
@@ -1,6 +1,7 @@
 #!/bin/bash
+set -e
 
-VERSION=0.3.0
+VERSION=0.3.1
 
 while [ $# -gt 0 ]; do
 	  case "$1" in
@@ -54,7 +55,7 @@ function getGenes {
 		echo $cmd
 	fi
 
-	docker run -i $DBMOUNT -v $(pwd):$(pwd) -v $WORK_DIR:$WORK_DIR -v ${OUTPUT_PATH}:${OUTPUT_PATH} quay.io/emgb/annotatedgenes2json:2.3.0 $cmd
+	docker run -i $DBMOUNT -v $(pwd):$(pwd) -v $WORK_DIR:$WORK_DIR -v ${OUTPUT_PATH}:${OUTPUT_PATH} quay.io/emgb/annotatedgenes2json:2.3.1 $cmd
 }
 
 

diff --git a/example_params/fullPipeline.yml b/example_params/fullPipeline.yml
@@ -187,6 +187,14 @@ steps:
 #          download:
 #            source: https://openstack.cebitec.uni-bielefeld.de:8080/databases/bacmet20_experimental.tar.zst
 #            md5sum: 57a6d328486f0acd63f7e984f739e8fe
+      ncbi_nr:
+        params: ' -s 1 --max-seqs 100 --max-accept 50 --alignment-mode 1 --exact-kmer-matching 1 --db-load-mode 3'
+        database:
+          download:
+            source: s3://databases/nr_2023-04-29_mmseqs_taxonomy/*
+            md5sum: 79b9fb6b3dada41e602d70e12e7351c2
+            s5cmd:
+              params: '--retry-count 30 --no-verify-ssl  --no-sign-request  --endpoint-url https://openstack.cebitec.uni-bielefeld.de:8080'
       bacmet20_predicted:
         params: ' -s 1 --max-seqs 100 --max-accept 50 --alignment-mode 1 --exact-kmer-matching 1 --db-load-mode 3'
         database: