Updated BLAST+ default DB version 5

biologger · Feb 6, 2020 · 9b37fc9 · 9b37fc9
1 parent b7c5f1f
commit 9b37fc9
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Showing 4 changed files with 8 additions and 9 deletions.
diff --git a/docs/pipelinesetup.md b/docs/pipelinesetup.md
@@ -10,8 +10,9 @@ To download the database with the update_blastdb perl script just click on the S
 
 #### Troubleshooting:
 The script changes to the "/blastdb" directory in the container and runs the command below
+(the default version of BLAST DBs for BLAST+ is 5)
 
-	$ update_blastdb.pl --passive --decompress --blastdb_version 5 nt_v5
+	$ update_blastdb.pl --passive --decompress nt
 
 To get possible hints or error messages you can run this command from a docker terminal.
 
@@ -24,7 +25,7 @@ __Example__
 * __Container__
 
 		$ cd /blastdb
-		$ update_blastdb.pl --passive --decompress --blastdb_version 5 nt_v5
+		$ update_blastdb.pl --passive --decompress nt
 
 As an alternative the python script __getblastdb.py__ can be used.
 

diff --git a/pipeline/gui/app/templates/blastdb.html b/pipeline/gui/app/templates/blastdb.html
@@ -13,7 +13,7 @@
 
   <h2> BLAST DB download (getblastdb.py)</h2>
   <p>
-    Download the nt_v5 BLAST DB (>60 GB) or the ref_prok_rep_genomes DB (~7 GB)
+    Download the nt BLAST DB (>60 GB) or the ref_prok_rep_genomes DB (~7 GB)
       <br>
       <br>
     {{ form.whichdb() }}   {{ form.whichdb.label }}
@@ -25,7 +25,7 @@ <h2> BLAST DB download (getblastdb.py)</h2>
     {{ form.get_blastdb() }}
   </p>
   <p>
-  Update the taxid list for the BLAST search with the nt BLAST database Version 5
+  Update the taxid list for the BLAST search with the BLAST database Version 5 option
    <br>
    <br>
   {{ form.update_txids() }}
@@ -38,7 +38,7 @@ <h3>Download the database with the NCBI update_blastdb perl script</h3>
   This may take some hours...
   <br>
   <br>
-  (update_blastdb.pl --passive --decompress --blastdb_version 5 nt_v5)
+  (update_blastdb.pl --passive --decompress nt)
   <br>
   <br>
   {{ form.update_blastdb() }}

diff --git a/pipeline/gui/daemon/daemonclass.py b/pipeline/gui/daemon/daemonclass.py
@@ -92,9 +92,7 @@ def command(self):
             level=logging.DEBUG, format="%(message)s")
         blastdb_dir = "/blastdb"
         os.chdir(blastdb_dir)
-        command = [
-            "update_blastdb.pl", "--passive", "--decompress",
-            "--blastdb_version", "5", "nt"]
+        command = ["update_blastdb.pl", "--passive", "--decompress", "nt"]
         process = subprocess.Popen(
             command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 

diff --git a/pipeline/speciesprimer.py b/pipeline/speciesprimer.py
@@ -3981,7 +3981,7 @@ def commandline():
         "The current settings files will be overwritten")
     # Version
     parser.add_argument(
-        "-V", "--version", action="version", version="%(prog)s 2.1.1")
+        "-V", "--version", action="version", version="%(prog)s 2.1.2")
     return parser