[med-svn] [Git][med-team/prokka][upstream] New upstream version 1.14.0+dfsg

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch upstream at Debian Med / prokka


Commits:
92dfdd23 by Michael R. Crusoe at 2019-09-13T11:39:37Z
New upstream version 1.14.0+dfsg
- - - - -


12 changed files:

- README.md
- bin/prokka
- bin/prokka-abricate_to_fasta_db
- bin/prokka-biocyc_to_fasta_db
- bin/prokka-cdd_to_hmm
- bin/prokka-clusters_to_hmm
- bin/prokka-genbank_to_fasta_db
- bin/prokka-genpept_to_fasta_db
- bin/prokka-hamap_to_hmm
- bin/prokka-tigrfams_to_hmm
- bin/prokka-uniprot_to_fasta_db
- test/plasmid.fna


Changes:

=====================================
README.md
=====================================
@@ -22,7 +22,7 @@ brew install brewsci/bio/prokka
 If you use [Conda](https://conda.io/docs/install/quick.html)
 you can use the [Bioconda channel](https://bioconda.github.io/):
 ```
-conda install -c conda-forge -c bioconda prokka
+conda install -c conda-forge -c bioconda -c defaults prokka
 ```
 
 ### Ubuntu/Debian/Mint


=====================================
bin/prokka
=====================================
@@ -19,8 +19,8 @@
 
 use strict;
 use warnings;
+###BREWCONDA###
 use FindBin;
-use lib "$FindBin::RealBin/../perl5"; # for bundled Perl modules
 use Cwd qw(abs_path);
 use File::Copy;
 use Time::Piece;
@@ -45,7 +45,7 @@ my @CMDLINE = ($0, @ARGV);
 my $OPSYS = $^O;
 my $BINDIR = "$FindBin::RealBin/../binaries/$OPSYS";
 my $EXE = $FindBin::RealScript;
-my $VERSION = "1.13.7";
+my $VERSION = "1.14.0";
 my $AUTHOR = 'Torsten Seemann <torsten.seemann at gmail.com>';
 my $URL = 'https://github.com/tseemann/prokka';
 my $PROKKA_PMID = '24642063';


=====================================
bin/prokka-abricate_to_fasta_db
=====================================
@@ -10,6 +10,7 @@
 #>Q92AT0 2.4.1.333~~~~~~1,2-beta-oligoglucan phosphorylase~~~COG3459
 #MTMLKEIKKADLSAAFYPSGELAWLKLKDIMLNQVIQNPLENRLSQIYVRAHVGDKIEIYPLLSRDAEVGFNENGVEYRGVVGPFRYSVQMHFHTRGWFYDVTVDGD
 
+###BREWCONDA###
 use Bio::SeqIO;
 use Data::Dumper;
 


=====================================
bin/prokka-biocyc_to_fasta_db
=====================================
@@ -1,6 +1,7 @@
 #!/usr/bin/env perl
 use strict;
 use warnings;
+###BREWCONDA###
 use Bio::SeqIO;
 use Data::Dumper;
 use Text::Unidecode qw(unidecode);


=====================================
bin/prokka-cdd_to_hmm
=====================================
@@ -2,6 +2,7 @@
 use strict;
 use warnings;
 use Data::Dumper;
+###BREWCONDA###
 use Bio::SeqIO;
 use Bio::AlignIO;
 use File::Temp qw(tempdir);


=====================================
bin/prokka-clusters_to_hmm
=====================================
@@ -1,6 +1,7 @@
 #!/usr/bin/env perl
 use strict;
 use warnings;
+###BREWCONDA###
 use Data::Dumper;
 use File::Temp qw(tempdir);
 


=====================================
bin/prokka-genbank_to_fasta_db
=====================================
@@ -1,6 +1,7 @@
 #!/usr/bin/env perl
 use strict;
 use warnings;
+###BREWCONDA###
 use Bio::SeqIO;
 use Bio::Tools::CodonTable;
 use Data::Dumper;


=====================================
bin/prokka-genpept_to_fasta_db
=====================================
@@ -1,6 +1,7 @@
 #!/usr/bin/env perl
 use strict;
 use warnings;
+###BREWCONDA###
 use Bio::SeqIO;
 
 my(@Options, $verbose, $format, $hypo, $idtag, $sep, $blank, $pseudo, $minlen);


=====================================
bin/prokka-hamap_to_hmm
=====================================
@@ -1,6 +1,7 @@
 #!/usr/bin/env perl
 use strict;
 use warnings;
+###BREWCONDA###
 use Bio::SeqIO;
 use Data::Dumper;
 use File::Temp qw(tempdir);


=====================================
bin/prokka-tigrfams_to_hmm
=====================================
@@ -2,7 +2,7 @@
 
 use strict;
 use warnings;
-
+###BREWCONDA###
 
 # These are most/all of the types of lines we need to clean up
 # so that the DESC line has a clean /product we can annotate with


=====================================
bin/prokka-uniprot_to_fasta_db
=====================================
@@ -1,6 +1,7 @@
 #!/usr/bin/env perl
 use strict;
 use warnings;
+###BREWCONDA###
 use SWISS::Entry;
 use SWISS::KW;
 #use SWISS::OC;


=====================================
test/plasmid.fna
=====================================
@@ -1,4 +1,4 @@
->gi|383315282|ref|NC_017032.1| Enterococcus faecium Aus0004 plasmid AUS0004_p1, complete sequence
+>NC_017032.1 Enterococcus faecium Aus0004 plasmid AUS0004_p1, complete sequence
 ATGAATGATTTTAATTATTACAAATCAAAAGAAATTTATCGTGAAAAATATTATCAAATGCCTAAGGTAT
 TTTTTACTAACGAAAAATACATGGATCTTTCAAATGATGCAAAAATTGCTTATATGCTACTTAAAGATCG
 ATTTGATTATTCAGTCAAAAATAACTGGGTAGATTCTGATGATAATATATTCTTCATATTCACAGTTGAA



View it on GitLab: https://salsa.debian.org/med-team/prokka/commit/92dfdd235ca133a1e9c98c1a93dab26e81d5b00a

-- 
View it on GitLab: https://salsa.debian.org/med-team/prokka/commit/92dfdd235ca133a1e9c98c1a93dab26e81d5b00a
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190913/33974f99/attachment-0001.html>