diff --git a/CHANGELOG b/CHANGELOG index e571f8d..fc7a171 100644 --- 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 index d13f6ed..d79045d 100755 --- 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 index db180a5..20ce9c7 100755 --- a/scripts/add_to_library.sh +++ b/scripts/add_to_library.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2017, Derrick Wood +# Copyright 2013-2019, Derrick Wood, Jennifer Lu # # 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 index 453678c..18b7a98 100755 --- a/scripts/build_kraken_db.sh +++ b/scripts/build_kraken_db.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2017, Derrick Wood +# Copyright 2013-2019, Derrick Wood, Jennifer Lu # # 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 index 63cc620..fac4d91 100755 --- a/scripts/check_for_jellyfish.sh +++ b/scripts/check_for_jellyfish.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2015, Derrick Wood +# Copyright 2013-2015, Derrick Wood, Jennifer Lu # # This file is part of the Kraken taxonomic sequence classification system. # diff --git a/scripts/clean_db.sh b/scripts/clean_db.sh index 85b9526..ece5079 100755 --- a/scripts/clean_db.sh +++ b/scripts/clean_db.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2015, Derrick Wood +# Copyright 2013-2015, Derrick Wood, Jennifer Lu # # 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 index 762c2e7..14c8113 100755 --- 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 +# Copyright 2013-2019, Derrick Wood, Jennifer Lu # # 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 index c502d2e..26f6f8d 100755 --- 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 +# Copyright 2013-2015, Derrick Wood, Jennifer Lu # # 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 index add3c18..d875a66 100755 --- a/scripts/download_genomic_library.sh +++ b/scripts/download_genomic_library.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2017, Derrick Wood +# Copyright 2013-2019, Derrick Wood, Jennifer Lu # # This file is part of the Kraken taxonomic sequence classification system. # diff --git a/scripts/download_taxonomy.sh b/scripts/download_taxonomy.sh index fb22f3e..dd2a68f 100755 --- a/scripts/download_taxonomy.sh +++ b/scripts/download_taxonomy.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2017, Derrick Wood +# Copyright 2013-2019, Derrick Wood, Jennifer Lu # # This file is part of the Kraken taxonomic sequence classification system. diff --git a/scripts/kraken b/scripts/kraken index 8da8309..4db2595 100755 --- a/scripts/kraken +++ b/scripts/kraken @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2015, Derrick Wood +# Copyright 2013-2015, Derrick Wood, Jennifer Lu # # 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 index 8f471a8..40ef06e 100755 --- a/scripts/kraken-build +++ b/scripts/kraken-build @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2017, Derrick Wood +# Copyright 2013-2019, Derrick Wood, Jennifer Lu # # 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 index 5ab01df..4cf47dd 100755 --- a/scripts/kraken-filter +++ b/scripts/kraken-filter @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013, Derrick Wood +# Copyright 2013, Derrick Wood, Jennifer Lu # # 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 index 526a167..f84d098 100755 --- a/scripts/kraken-mpa-report +++ b/scripts/kraken-mpa-report @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2015, Derrick Wood +# Copyright 2013-2015, Derrick Wood, Jennifer Lu # # 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 index 582a819..866ca18 100755 --- a/scripts/kraken-report +++ b/scripts/kraken-report @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2015, Derrick Wood +# Copyright 2013-2015, Derrick Wood, Jennifer Lu # # 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 index 46c9102..82fc38b 100755 --- a/scripts/kraken-translate +++ b/scripts/kraken-translate @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2015, Derrick Wood +# Copyright 2013-2015, Derrick Wood, Jennifer Lu # # 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 index f7e01b2..ef55bb3 100644 --- a/scripts/krakenlib.pm +++ b/scripts/krakenlib.pm @@ -1,6 +1,6 @@ package krakenlib; -# Copyright 2013-2017, Derrick Wood +# Copyright 2013-2019, Derrick Wood, Jennifer Lu # # 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 index 376ebf2..1acc7d1 100755 --- 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 +# Copyright 2013-2019, Derrick Wood, Jennifer Lu # # This file is part of the Kraken taxonomic sequence classification system. diff --git a/scripts/read_merger.pl b/scripts/read_merger.pl index 1471f4a..f41b4d5 100755 --- a/scripts/read_merger.pl +++ b/scripts/read_merger.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2015, Derrick Wood +# Copyright 2013-2015, Derrick Wood, Jennifer Lu # # 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 index 102a5d9..d8a4c9e 100755 --- 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 +# Copyright 2013-2015, Derrick Wood, Jennifer Lu # # 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 index b3b6ab4..07e74ef 100755 --- 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 +# Copyright 2013-2019, Derrick Wood, Jennifer Lu # # 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 index 4f69ee4..dea08f6 100755 --- 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 +# Copyright 2013-2019, Derrick Wood, Jennifer Lu # # This file is part of the Kraken taxonomic sequence classification system. diff --git a/scripts/shrink_db.sh b/scripts/shrink_db.sh index a14249f..688fe56 100755 --- a/scripts/shrink_db.sh +++ b/scripts/shrink_db.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2015, Derrick Wood +# Copyright 2013-2015, Derrick Wood, Jennifer Lu # # This file is part of the Kraken taxonomic sequence classification system. # diff --git a/scripts/standard_installation.sh b/scripts/standard_installation.sh index 731cd7f..4733a8f 100755 --- a/scripts/standard_installation.sh +++ b/scripts/standard_installation.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2017, Derrick Wood +# Copyright 2013-2019, Derrick Wood, Jennifer Lu # # This file is part of the Kraken taxonomic sequence classification system. # diff --git a/scripts/upgrade_db.sh b/scripts/upgrade_db.sh index b59ba63..4adffa9 100755 --- a/scripts/upgrade_db.sh +++ b/scripts/upgrade_db.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2015, Derrick Wood +# Copyright 2013-2015, Derrick Wood, Jennifer Lu # # 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 index 0bb5cdf..98e4186 100755 --- 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 +# Copyright 2013-2015, Derrick Wood, Jennifer Lu # # This file is part of the Kraken taxonomic sequence classification system. # diff --git a/src/classify.cpp b/src/classify.cpp index 3527f91..5836570 100644 --- a/src/classify.cpp +++ b/src/classify.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013-2015, Derrick Wood + * Copyright 2013-2019, Derrick Wood, Jennifer Lu * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/db_shrink.cpp b/src/db_shrink.cpp index 164073f..cd64fe3 100644 --- a/src/db_shrink.cpp +++ b/src/db_shrink.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013-2015, Derrick Wood + * Copyright 2013-2019, Derrick Wood, Jennifer Lu * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/db_sort.cpp b/src/db_sort.cpp index 1bafef3..dacb85c 100644 --- a/src/db_sort.cpp +++ b/src/db_sort.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013-2015, Derrick Wood + * Copyright 2013-2019, Derrick Wood, Jennifer Lu * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/kmer_estimator.cpp b/src/kmer_estimator.cpp index 9562893..c7b8ea6 100644 --- a/src/kmer_estimator.cpp +++ b/src/kmer_estimator.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013-2017, Derrick Wood + * Copyright 2013-2017, Derrick Wood, Jennifer Lu * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/kraken_headers.hpp b/src/kraken_headers.hpp index bca9858..9d8346b 100644 --- a/src/kraken_headers.hpp +++ b/src/kraken_headers.hpp @@ -1,5 +1,5 @@ /* - * Copyright 2013-2015, Derrick Wood + * Copyright 2013-2019, Derrick Wood, Jennifer Lu * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/krakendb.cpp b/src/krakendb.cpp index 83e71b3..a987b08 100644 --- a/src/krakendb.cpp +++ b/src/krakendb.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013-2015, Derrick Wood + * Copyright 2013-2019, Derrick Wood, Jennifer Lu * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/krakendb.hpp b/src/krakendb.hpp index c30eeb5..a415fed 100644 --- a/src/krakendb.hpp +++ b/src/krakendb.hpp @@ -1,5 +1,5 @@ /* - * Copyright 2013-2015, Derrick Wood + * Copyright 2013-2019, Derrick Wood, Jennifer Lu * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/krakenutil.cpp b/src/krakenutil.cpp index a00e6bb..a0f79a9 100644 --- a/src/krakenutil.cpp +++ b/src/krakenutil.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013-2015, Derrick Wood + * Copyright 2013-2019, Derrick Wood, Jennifer Lu * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/krakenutil.hpp b/src/krakenutil.hpp index 196ee1d..254e595 100644 --- a/src/krakenutil.hpp +++ b/src/krakenutil.hpp @@ -1,5 +1,5 @@ /* - * Copyright 2013-2015, Derrick Wood + * Copyright 2013-2019, Derrick Wood, Jennifer Lu * * 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 index 30b3091..3610663 100644 --- 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 + * Copyright 2013-2019, Derrick Wood, Jennifer Lu * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/quickfile.cpp b/src/quickfile.cpp index ddabe9a..4b3e9d7 100644 --- a/src/quickfile.cpp +++ b/src/quickfile.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013-2015, Derrick Wood + * Copyright 2013-2019, Derrick Wood, Jennifer Lu * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/quickfile.hpp b/src/quickfile.hpp index 5533580..06bde8e 100644 --- a/src/quickfile.hpp +++ b/src/quickfile.hpp @@ -1,5 +1,5 @@ /* - * Copyright 2013-2015, Derrick Wood + * Copyright 2013-2019, Derrick Wood, Jennifer Lu * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/seqreader.cpp b/src/seqreader.cpp index 78c1442..6b96cf2 100644 --- a/src/seqreader.cpp +++ b/src/seqreader.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013-2015, Derrick Wood + * Copyright 2013-2019, Derrick Wood, Jennifer Lu * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/seqreader.hpp b/src/seqreader.hpp index 40c1b77..8dad459 100644 --- a/src/seqreader.hpp +++ b/src/seqreader.hpp @@ -1,5 +1,5 @@ /* - * Copyright 2013-2015, Derrick Wood + * Copyright 2013-2019, Derrick Wood, Jennifer Lu * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/set_lcas.cpp b/src/set_lcas.cpp index 027a386..b870a9d 100644 --- a/src/set_lcas.cpp +++ b/src/set_lcas.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013-2015, Derrick Wood + * Copyright 2013-2019, Derrick Wood, Jennifer Lu * * This file is part of the Kraken taxonomic sequence classification system. *