CHANGELOG

+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

debian/changelog

+kraken (1.1.1-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+
+ -- Andreas Tille <tille@debian.org>  Thu, 01 Aug 2019 13:29:55 +0200
+
 kraken (1.1-3) unstable; urgency=medium
 
   [ Jelmer Vernooij ]

debian/compat

-11

debian/control

@@ -3,9 +3,9 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                jellyfish1
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/kraken
 Vcs-Git: https://salsa.debian.org/med-team/kraken.git
 Homepage: http://ccb.jhu.edu/software/kraken/

debian/patches/kraken_tmp_dir.patch

@@ -7,7 +7,7 @@ Description: Some changes needed to differentiate packaging target dir and
 +++ b/install_kraken.sh
 @@ -21,7 +21,7 @@ set -e
  
- VERSION="1.0"
+ VERSION="1.1.1"
  
 -if [ -z "$1" ] || [ -n "$2" ]
 +if [ -z "$1" ] # || [ -n "$2" ]

install_kraken.sh

@@ -19,7 +19,7 @@
 
 set -e
 
-VERSION="1.0"
+VERSION="1.1.1"
 
 if [ -z "$1" ] || [ -n "$2" ]
 then

scripts/add_to_library.sh

 #!/bin/bash
 
-# Copyright 2013-2017, Derrick Wood <dwood@cs.jhu.edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

scripts/build_kraken_db.sh

 #!/bin/bash
 
-# Copyright 2013-2017, Derrick Wood <dwood@cs.jhu.edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

scripts/check_for_jellyfish.sh

 #!/bin/bash
 
-# Copyright 2013-2015, Derrick Wood <dwood@cs.jhu.edu>
+# Copyright 2013-2015, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

scripts/clean_db.sh

 #!/bin/bash
 
-# Copyright 2013-2015, Derrick Wood <dwood@cs.jhu.edu>
+# Copyright 2013-2015, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

scripts/convert_gb_to_fa.pl

 #!/usr/bin/env perl
 
-# Copyright 2013-2017, Derrick Wood <dwood@cs.jhu.edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

scripts/cp_into_tempfile.pl

 #!/usr/bin/env perl
 
-# Copyright 2013-2015, Derrick Wood <dwood@cs.jhu.edu>
+# Copyright 2013-2015, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

scripts/download_genomic_library.sh

 #!/bin/bash
 
-# Copyright 2013-2017, Derrick Wood <dwood@cs.jhu.edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #

scripts/download_taxonomy.sh

 #!/bin/bash
 
-# Copyright 2013-2017, Derrick Wood <dwood@cs.jhu.edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 
@@ -19,9 +19,9 @@ cd "$TAXONOMY_DIR"
 
 if [ ! -e "accmap.dlflag" ]
 then
-  wget $FTP_SERVER/pub/taxonomy/accession2taxid/nucl_est.accession2taxid.gz
+  #wget $FTP_SERVER/pub/taxonomy/accession2taxid/nucl_est.accession2taxid.gz
   wget $FTP_SERVER/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz
-  wget $FTP_SERVER/pub/taxonomy/accession2taxid/nucl_gss.accession2taxid.gz
+  #wget $FTP_SERVER/pub/taxonomy/accession2taxid/nucl_gss.accession2taxid.gz
   wget $FTP_SERVER/pub/taxonomy/accession2taxid/nucl_wgs.accession2taxid.gz
   touch accmap.dlflag
   echo "Downloaded accession to taxon map(s)"

scripts/kraken

 #!/usr/bin/env perl
 
-# Copyright 2013-2015, Derrick Wood <dwood@cs.jhu.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;
 }
 

scripts/kraken-build

 #!/usr/bin/env perl
 
-# Copyright 2013-2017, Derrick Wood <dwood@cs.jhu.edu>
+# Copyright 2013-2019, Derrick Wood, Jennifer Lu <jlu26@jhmi.edu>
 #
 # This file is part of the Kraken taxonomic sequence classification system.
 #
@@ -52,6 +52,7 @@ my (
   $hash_size,
   $max_db_size,
   $work_on_disk,
+  $use_wget,
   $shrink_block_offset,
 
   $dl_taxonomy,
@@ -96,6 +97,7 @@ GetOptions(
   "new-db=s", \$new_db,
   "jellyfish-hash-size=s", \$hash_size,
   "max-db-size=s", \$max_db_size,
+  "use-wget" => \$use_wget,
   "work-on-disk", \$work_on_disk,
   "shrink-block-offset=i", \$shrink_block_offset,
 
@@ -159,7 +161,7 @@ $ENV{"KRAKEN_KMER_LEN"} = $kmer_len;
 $ENV{"KRAKEN_HASH_SIZE"} = $hash_size;
 $ENV{"KRAKEN_MAX_DB_SIZE"} = $max_db_size;
 $ENV{"KRAKEN_WORK_ON_DISK"} = $work_on_disk;
-
+$ENV{"KRAKEN_USE_WGET"} = $use_wget ? 1 : "";
 if ($dl_taxonomy) {
   download_taxonomy();
 }
@@ -230,6 +232,8 @@ Options:
   --max-db-size SIZE         Shrink the DB before full build, making sure
                              database and index together use <= SIZE gigabytes
                              (build task only)
+  --use-wget                 Use wget for downloading instead of RSYNC; used with
+                             --download-library/--standard
   --shrink-block-offset NUM  When shrinking, select the k-mer that is NUM
                              positions from the end of a block of k-mers
                              (default: 1)
@@ -245,7 +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;
 }
 

scripts/kraken-filter

 #!/usr/bin/env perl
 
-# Copyright 2013, Derrick Wood <dwood@cs.jhu.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;
 }
 

scripts/kraken-mpa-report

 #!/usr/bin/env perl
 
-# Copyright 2013-2015, Derrick Wood <dwood@cs.jhu.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;
 }
 

scripts/kraken-report

 #!/usr/bin/env perl
 
-# Copyright 2013-2015, Derrick Wood <dwood@cs.jhu.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;
 }
 

scripts/kraken-translate

 #!/usr/bin/env perl
 
-# Copyright 2013-2015, Derrick Wood <dwood@cs.jhu.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;
 }