Skip to content

Commit

Permalink
Updated version number to 1.1.1
Browse files Browse the repository at this point in the history
Fixed Copyright and emails
  • Loading branch information
Jennifer Lu committed May 4, 2019
1 parent 41b5e9d commit e343539
Show file tree
Hide file tree
Showing 41 changed files with 51 additions and 46 deletions.
5 changes: 5 additions & 0 deletions CHANGELOG
Original file line number Diff line number Diff line change
@@ -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
Expand Down
2 changes: 1 addition & 1 deletion install_kraken.sh
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@

set -e

VERSION="1.0"
VERSION="1.1.1"

if [ -z "$1" ] || [ -n "$2" ]
then
Expand Down
2 changes: 1 addition & 1 deletion scripts/add_to_library.sh
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down
2 changes: 1 addition & 1 deletion scripts/build_kraken_db.sh
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down
2 changes: 1 addition & 1 deletion scripts/check_for_jellyfish.sh
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down
2 changes: 1 addition & 1 deletion scripts/clean_db.sh
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down
2 changes: 1 addition & 1 deletion scripts/convert_gb_to_fa.pl
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down
2 changes: 1 addition & 1 deletion scripts/cp_into_tempfile.pl
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down
2 changes: 1 addition & 1 deletion scripts/download_genomic_library.sh
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down
2 changes: 1 addition & 1 deletion scripts/download_taxonomy.sh
Original file line number Diff line number Diff line change
@@ -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.

Expand Down
4 changes: 2 additions & 2 deletions scripts/kraken
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down Expand Up @@ -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;
}

Expand Down
4 changes: 2 additions & 2 deletions scripts/kraken-build
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down Expand Up @@ -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;
}

Expand Down
4 changes: 2 additions & 2 deletions scripts/kraken-filter
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down Expand Up @@ -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;
}

Expand Down
4 changes: 2 additions & 2 deletions scripts/kraken-mpa-report
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down Expand Up @@ -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;
}

Expand Down
4 changes: 2 additions & 2 deletions scripts/kraken-report
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down Expand Up @@ -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;
}

Expand Down
4 changes: 2 additions & 2 deletions scripts/kraken-translate
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down Expand Up @@ -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;
}

Expand Down
2 changes: 1 addition & 1 deletion scripts/krakenlib.pm
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down
2 changes: 1 addition & 1 deletion scripts/lookup_accession_numbers.pl
Original file line number Diff line number Diff line change
@@ -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.

Expand Down
2 changes: 1 addition & 1 deletion scripts/read_merger.pl
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down
2 changes: 1 addition & 1 deletion scripts/report_gi_numbers.pl
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down
2 changes: 1 addition & 1 deletion scripts/rsync_from_ncbi.pl
Original file line number Diff line number Diff line change
@@ -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.

Expand Down
2 changes: 1 addition & 1 deletion scripts/scan_fasta_file.pl
Original file line number Diff line number Diff line change
@@ -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.

Expand Down
2 changes: 1 addition & 1 deletion scripts/shrink_db.sh
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down
2 changes: 1 addition & 1 deletion scripts/standard_installation.sh
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down
2 changes: 1 addition & 1 deletion scripts/upgrade_db.sh
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down
2 changes: 1 addition & 1 deletion scripts/verify_gi_numbers.pl
Original file line number Diff line number Diff line change
@@ -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.
#
Expand Down
2 changes: 1 addition & 1 deletion src/classify.cpp
Original file line number Diff line number Diff line change
@@ -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.
*
Expand Down
2 changes: 1 addition & 1 deletion src/db_shrink.cpp
Original file line number Diff line number Diff line change
@@ -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.
*
Expand Down
2 changes: 1 addition & 1 deletion src/db_sort.cpp
Original file line number Diff line number Diff line change
@@ -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.
*
Expand Down
2 changes: 1 addition & 1 deletion src/kmer_estimator.cpp
Original file line number Diff line number Diff line change
@@ -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.
*
Expand Down
2 changes: 1 addition & 1 deletion src/kraken_headers.hpp
Original file line number Diff line number Diff line change
@@ -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.
*
Expand Down
2 changes: 1 addition & 1 deletion src/krakendb.cpp
Original file line number Diff line number Diff line change
@@ -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.
*
Expand Down
2 changes: 1 addition & 1 deletion src/krakendb.hpp
Original file line number Diff line number Diff line change
@@ -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.
*
Expand Down
2 changes: 1 addition & 1 deletion src/krakenutil.cpp
Original file line number Diff line number Diff line change
@@ -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.
*
Expand Down
2 changes: 1 addition & 1 deletion src/krakenutil.hpp
Original file line number Diff line number Diff line change
@@ -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.
*
Expand Down
2 changes: 1 addition & 1 deletion src/make_seqid_to_taxid_map.cpp
Original file line number Diff line number Diff line change
@@ -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.
*
Expand Down
2 changes: 1 addition & 1 deletion src/quickfile.cpp
Original file line number Diff line number Diff line change
@@ -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.
*
Expand Down
2 changes: 1 addition & 1 deletion src/quickfile.hpp
Original file line number Diff line number Diff line change
@@ -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.
*
Expand Down
2 changes: 1 addition & 1 deletion src/seqreader.cpp
Original file line number Diff line number Diff line change
@@ -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.
*
Expand Down
2 changes: 1 addition & 1 deletion src/seqreader.hpp
Original file line number Diff line number Diff line change
@@ -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.
*
Expand Down
2 changes: 1 addition & 1 deletion src/set_lcas.cpp
Original file line number Diff line number Diff line change
@@ -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.
*
Expand Down

0 comments on commit e343539

Please sign in to comment.