Updated version number to 1.1.1

Fixed Copyright and emails
DerrickWood · May 4, 2019 · e343539 · e343539
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diff --git a/CHANGELOG b/CHANGELOG
@@ -1,3 +1,8 @@
+v 1.1.1:
+* fixed download of taxonomy with NCBI taxonomy update est --> gb 
+* added --use-wget for downloading of data from NCBI instead of rsync
+* updated Copyright and emails 
+
 v1.1:
 * added --out-fmt paired and --out-fmt interleaved to allow paired reads
   to be separated when using --[un]classified-out options

diff --git a/install_kraken.sh b/install_kraken.sh
@@ -19,7 +19,7 @@
 
 set -e
 
-VERSION="1.0"
+VERSION="1.1.1"
 
 if [ -z "$1" ] || [ -n "$2" ]
 then

diff --git a/scripts/add_to_library.sh b/scripts/add_to_library.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013-2017, Derrick Wood <[email protected].edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/build_kraken_db.sh b/scripts/build_kraken_db.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013-2017, Derrick Wood <[email protected].edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/check_for_jellyfish.sh b/scripts/check_for_jellyfish.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013-2015, Derrick Wood <[email protected].edu>
+# Copyright 2013-2015, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/clean_db.sh b/scripts/clean_db.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013-2015, Derrick Wood <[email protected].edu>
+# Copyright 2013-2015, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/convert_gb_to_fa.pl b/scripts/convert_gb_to_fa.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Copyright 2013-2017, Derrick Wood <[email protected].edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/cp_into_tempfile.pl b/scripts/cp_into_tempfile.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Copyright 2013-2015, Derrick Wood <[email protected].edu>
+# Copyright 2013-2015, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/download_genomic_library.sh b/scripts/download_genomic_library.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013-2017, Derrick Wood <[email protected].edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/download_taxonomy.sh b/scripts/download_taxonomy.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013-2017, Derrick Wood <[email protected].edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 

diff --git a/scripts/kraken b/scripts/kraken
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Copyright 2013-2015, Derrick Wood <[email protected].edu>
+# Copyright 2013-2015, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #
@@ -253,7 +253,7 @@ sub display_help {
 
 sub display_version {
   print "Kraken version #####=VERSION=#####\n";
-  print "Copyright 2013-2015, Derrick Wood (dwood\@cs.jhu.edu)\n";
+  print "Copyright 2013-2019, Derrick Wood, Jennifer Lu (jlu26\@jhmi.edu)\n";
   exit 0;
 }
 

diff --git a/scripts/kraken-build b/scripts/kraken-build
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Copyright 2013-2017, Derrick Wood <[email protected].edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #
@@ -249,7 +249,7 @@ sub display_help {
 
 sub display_version {
   print "Kraken version #####=VERSION=#####\n";
-  print "Copyright 2013-2015, Derrick Wood (dwood\@cs.jhu.edu)\n";
+  print "Copyright 2013-2019, Derrick Wood, Jennifer Lu (jlu26\@jhmi.edu))\n";
   exit 0;
 }
 

diff --git a/scripts/kraken-filter b/scripts/kraken-filter
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Copyright 2013, Derrick Wood <[email protected].edu>
+# Copyright 2013, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #
@@ -73,7 +73,7 @@ sub display_help {
 
 sub display_version {
   print "Kraken version #####=VERSION=#####\n";
-  print "Copyright 2013-2015, Derrick Wood (dwood\@cs.jhu.edu)\n";
+  print "Copyright 2013-2019, Derrick Wood, Jennifer Lu (jlu26\@jhmi.edu)\n";
   exit 0;
 }
 

diff --git a/scripts/kraken-mpa-report b/scripts/kraken-mpa-report
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Copyright 2013-2015, Derrick Wood <[email protected].edu>
+# Copyright 2013-2015, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #
@@ -80,7 +80,7 @@ sub display_help {
 
 sub display_version {
   print "Kraken version #####=VERSION=#####\n";
-  print "Copyright 2013-2015, Derrick Wood (dwood\@cs.jhu.edu)\n";
+  print "Copyright 2013-2019, Derrick Wood, Jennifer Lu (jlu26\@jhmi.edu)\n";
   exit 0;
 }
 

diff --git a/scripts/kraken-report b/scripts/kraken-report
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Copyright 2013-2015, Derrick Wood <[email protected].edu>
+# Copyright 2013-2015, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #
@@ -67,7 +67,7 @@ sub display_help {
 
 sub display_version {
   print "Kraken version #####=VERSION=#####\n";
-  print "Copyright 2013-2015, Derrick Wood (dwood\@cs.jhu.edu)\n";
+  print "Copyright 2013-2019, Derrick Wood, Jennifer Lu (jlu26\@jhmi.edu)\n";
   exit 0;
 }
 

diff --git a/scripts/kraken-translate b/scripts/kraken-translate
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Copyright 2013-2015, Derrick Wood <[email protected].edu>
+# Copyright 2013-2015, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #
@@ -67,7 +67,7 @@ sub display_help {
 
 sub display_version {
   print "Kraken version #####=VERSION=#####\n";
-  print "Copyright 2013-2015, Derrick Wood (dwood\@cs.jhu.edu)\n";
+  print "Copyright 2013-2019, Derrick Wood, Jennifer Lu (jlu26\@jhmi.edu)\n";
   exit 0;
 }
 

diff --git a/scripts/krakenlib.pm b/scripts/krakenlib.pm
@@ -1,6 +1,6 @@
 package krakenlib;
 
-# Copyright 2013-2017, Derrick Wood <[email protected].edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/lookup_accession_numbers.pl b/scripts/lookup_accession_numbers.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Copyright 2013-2017, Derrick Wood <[email protected].edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 

diff --git a/scripts/read_merger.pl b/scripts/read_merger.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Copyright 2013-2015, Derrick Wood <[email protected].edu>
+# Copyright 2013-2015, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/report_gi_numbers.pl b/scripts/report_gi_numbers.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Copyright 2013-2015, Derrick Wood <[email protected].edu>
+# Copyright 2013-2015, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/rsync_from_ncbi.pl b/scripts/rsync_from_ncbi.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Copyright 2013-2017, Derrick Wood <[email protected].edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 

diff --git a/scripts/scan_fasta_file.pl b/scripts/scan_fasta_file.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Copyright 2013-2017, Derrick Wood <[email protected].edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 

diff --git a/scripts/shrink_db.sh b/scripts/shrink_db.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013-2015, Derrick Wood <[email protected].edu>
+# Copyright 2013-2015, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/standard_installation.sh b/scripts/standard_installation.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013-2017, Derrick Wood <[email protected].edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/upgrade_db.sh b/scripts/upgrade_db.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright 2013-2015, Derrick Wood <[email protected].edu>
+# Copyright 2013-2015, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/scripts/verify_gi_numbers.pl b/scripts/verify_gi_numbers.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Copyright 2013-2015, Derrick Wood <[email protected].edu>
+# Copyright 2013-2015, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

diff --git a/src/classify.cpp b/src/classify.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2015, Derrick Wood <[email protected].edu>
+ * Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/db_shrink.cpp b/src/db_shrink.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2015, Derrick Wood <[email protected].edu>
+ * Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/db_sort.cpp b/src/db_sort.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2015, Derrick Wood <[email protected].edu>
+ * Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/kmer_estimator.cpp b/src/kmer_estimator.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2017, Derrick Wood <[email protected].edu>
+ * Copyright 2013-2017, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/kraken_headers.hpp b/src/kraken_headers.hpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2015, Derrick Wood <[email protected].edu>
+ * Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/krakendb.cpp b/src/krakendb.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2015, Derrick Wood <[email protected].edu>
+ * Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/krakendb.hpp b/src/krakendb.hpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2015, Derrick Wood <[email protected].edu>
+ * Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/krakenutil.cpp b/src/krakenutil.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2015, Derrick Wood <[email protected].edu>
+ * Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/krakenutil.hpp b/src/krakenutil.hpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2015, Derrick Wood <[email protected].edu>
+ * Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/make_seqid_to_taxid_map.cpp b/src/make_seqid_to_taxid_map.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2015, Derrick Wood <[email protected].edu>
+ * Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/quickfile.cpp b/src/quickfile.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2015, Derrick Wood <[email protected].edu>
+ * Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/quickfile.hpp b/src/quickfile.hpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2015, Derrick Wood <[email protected].edu>
+ * Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/seqreader.cpp b/src/seqreader.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2015, Derrick Wood <[email protected].edu>
+ * Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/seqreader.hpp b/src/seqreader.hpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2015, Derrick Wood <[email protected].edu>
+ * Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *

diff --git a/src/set_lcas.cpp b/src/set_lcas.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2015, Derrick Wood <[email protected].edu>
+ * Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
  *
  * This file is part of the Kraken taxonomic sequence classification system.
  *