[med-svn] [Git][med-team/prokka][master] 8 commits: New upstream version 1.14.0+dfsg
Michael R. Crusoe
gitlab at salsa.debian.org
Fri Sep 13 14:33:56 BST 2019
Michael R. Crusoe pushed to branch master at Debian Med / prokka
Commits:
92dfdd23 by Michael R. Crusoe at 2019-09-13T11:39:37Z
New upstream version 1.14.0+dfsg
- - - - -
56246504 by Michael R. Crusoe at 2019-09-13T11:39:54Z
Update upstream source from tag 'upstream/1.14.0+dfsg'
Update to upstream version '1.14.0+dfsg'
with Debian dir 458f9613ed6fdaa827fc2a0b53289b8bf88ba7a8
- - - - -
dbb92a98 by Michael R. Crusoe at 2019-09-13T11:39:54Z
New upstream version
- - - - -
ac2cbc41 by Michael R. Crusoe at 2019-09-13T11:39:55Z
debhelper-compat 12
- - - - -
6a0a9397 by Michael R. Crusoe at 2019-09-13T11:39:57Z
Standards-Version: 4.4.0
- - - - -
eff0b5b6 by Michael R. Crusoe at 2019-09-13T11:43:14Z
release 1.14.0+dfsg-1
- - - - -
58b4e0d8 by Michael R. Crusoe at 2019-09-13T13:31:07Z
add AutoPkgTest
- - - - -
4f424b3b by Michael R. Crusoe at 2019-09-13T13:33:25Z
build-dep on unreleased libbio-searchio-hmmer-perl
- - - - -
20 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
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/hmmer_not_hmmer3
- debian/patches/series
- debian/patches/set-db-dir
- + debian/tests/control
- + debian/tests/sample-programs
- 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;
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+prokka (1.14.0+dfsg-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ * add missing dependencies: default-jre, less
+ * Fix path to hmmer v3
+ * Add autopkgtest
+ * with recent libbio-perl-perl with need a separate
+ libbio-searchio-hmmer-perl package
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Fri, 13 Sep 2019 13:42:10 +0200
+
prokka (1.13.7+dfsg-1) unstable; urgency=medium
* New upstream release.
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12
=====================================
debian/control
=====================================
@@ -4,9 +4,9 @@ Uploaders: Michael R. Crusoe <mcrusoe at msu.edu>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
libswiss-perl
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/prokka
Vcs-Git: https://salsa.debian.org/med-team/prokka.git
Homepage: http://www.vicbioinformatics.com/software.prokka.shtml
@@ -24,7 +24,10 @@ Depends: ${misc:Depends},
ncbi-tools-bin,
infernal,
libswiss-perl,
- libxml-simple-perl
+ libxml-simple-perl,
+ default-jre,
+ less,
+ libbio-searchio-hmmer-perl
Description: rapid annotation of prokaryotic genomes
A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a
quad-core computer, and scales well to 32 core SMP systems. It produces GFF3,
=====================================
debian/patches/hmmer_not_hmmer3
=====================================
@@ -0,0 +1,22 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: Use the Debian binary name for hmmer v3
+--- prokka.orig/bin/prokka
++++ prokka/bin/prokka
+@@ -922,7 +922,7 @@
+ push @database, {
+ DB => $dbfile,
+ SRC => "protein motif:$name:",
+- FMT => 'hmmer3',
++ FMT => 'hmmer',
+ CMD => $HMMER3CMD,
+ VERSION => 3, # without this, latest Bioperl goes into infinite loop
+ }
+@@ -965,7 +965,7 @@
+ unshift @database, {
+ DB => $hmms,
+ SRC => $compliant ? "" : "protein motif:$src:",
+- FMT => 'hmmer3',
++ FMT => 'hmmer',
+ CMD => $HMMER3CMD,
+ VERSION => 3, # without this, latest Bioperl goes into infinite loop
+ };
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
set-db-dir
+hmmer_not_hmmer3
=====================================
debian/patches/set-db-dir
=====================================
@@ -6,8 +6,8 @@ Last-Update: 2015-02-21
---
---- a/bin/prokka-build_kingdom_dbs
-+++ b/bin/prokka-build_kingdom_dbs
+--- prokka.orig/bin/prokka-build_kingdom_dbs
++++ prokka/bin/prokka-build_kingdom_dbs
@@ -4,7 +4,7 @@
URL="ftp://ftp.ebi.edu.au/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/"
@@ -17,7 +17,7 @@ Last-Update: 2015-02-21
echo "*** NOTICE ***"
echo "This script is about to download data from the Internet and overwrite your existing Prokka BLAST databases."
-@@ -28,7 +28,7 @@ for K in Viruses Archaea Bacteria ; do
+@@ -28,7 +28,7 @@
wget -q -O - "$DAT" | \
gunzip | \
@@ -26,14 +26,14 @@ Last-Update: 2015-02-21
makeblastdb -in - -dbtype prot -title "Prokka $K" -hash_index -out "$DIR/sprot"
# If you want a copy of the sprot file too (we do for git distribution)
---- a/bin/prokka
-+++ b/bin/prokka
-@@ -232,7 +232,7 @@ my(@Options, $quiet, $debug, $kingdom, $
+--- prokka.orig/bin/prokka
++++ prokka/bin/prokka
+@@ -232,7 +232,7 @@
$rfam, $norrna, $notrna, $rnammer, $rawproduct, $noanno, $accver,
$metagenome, $compliant, $listdb, $citation);
-$dbdir = $ENV{'PROKKA_DBDIR'} || abs_path("$FindBin::RealBin/../db");
-+$dbdir = "/var/lib/prokka/db";
++$dbdir = $ENV{'PROKKA_DBDIR'} || "/var/lib/prokka/db";
setOptions();
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: sample-programs
+Depends: @, bash, wget, ca-certificates
+Restrictions: allow-stderr
=====================================
debian/tests/sample-programs
=====================================
@@ -0,0 +1,11 @@
+#!/bin/bash -ex
+pkg=prokka
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+fi
+sh /usr/share/doc/prokka/get-additional-data
+prokka --version
+prokka --help
+prokka --listdb
+prokka --cpus $(nproc) --outdir "${AUTOPKGTEST_TMP}"/asm --prefix asm test/plasmid.fna
+grep '>' "${AUTOPKGTEST_TMP}"/asm/asm.fna
=====================================
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/compare/afc9ba11fd2363e9a6a9632fa0b5cf93d077ba81...4f424b3ba681a463d52a458d9f76fd74b5f085ad
--
View it on GitLab: https://salsa.debian.org/med-team/prokka/compare/afc9ba11fd2363e9a6a9632fa0b5cf93d077ba81...4f424b3ba681a463d52a458d9f76fd74b5f085ad
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