updating groot-core-db

will-rowe · Mar 27, 2018 · 1960bcb · 1960bcb
1 parent afdd87a
commit 1960bcb
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/cmd/get.go b/cmd/get.go
@@ -41,7 +41,7 @@ var md5sums = map[string]string{
 	"resfinder.90":     "de34ab790693cb7c7b656d537ec40f05",
 	"card.90":          "3e8a7b56fb7ce1c857299decac2d71c2",
 	"groot-db.90":      "2cbbe9a89c2ce23c09575198832250d3",
-	"groot-core-db.90": "93e09c4b93310f4b54f9ef11c5e2d42b",
+	"groot-core-db.90": "f3cac49ff44624a26ea2d92171a73174",
 }
 
 // url to download databases from

diff --git a/db/clustered-ARG-databases/groot-core-db.90.tar b/db/clustered-ARG-databases/groot-core-db.90.tar
diff --git a/db/groot-database/make-groot-dbs.sh b/db/groot-database/make-groot-dbs.sh
@@ -62,7 +62,7 @@ cd ..
 # Create the groot-core-db
 mkdir groot-core-db.90 && cd $_
 cat ../*.fna > all-args.fasta
-vsearch --cluster_size ../all-args.fasta --id 1 --msaout MSA.tmp
+vsearch --cluster_size ../all-args.fasta --id 0.99 --msaout MSA.tmp
 awk '!a[$0]++ {of="./cluster-" ++fc ".msa"; print $0 >> of ; close(of)}' RS= ORS="\n\n" MSA.tmp && rm MSA.tmp
 for i in *.msa
 do

diff --git a/testing/run_travis_tests.sh b/testing/run_travis_tests.sh
@@ -4,10 +4,10 @@
 go build
 
 # download the database
-./groot get -d arg-annot
+./groot get -d groot-core-db
 
 # index the example
-./groot index -p 1 -i ./arg-annot.90 -o test-index
+./groot index -p 1 -i ./groot-core-db.90 -o test-index
 
 # align the test reads
 ./groot align -p 1 -i test-index -f testing/full-argannot-perfect-reads-small.fq.gz > out.bam