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 <[email protected]>'; 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.
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