[med-svn] [roary] 01/04: New upstream version 3.11.3+dfsg
Sascha Steinbiss
satta at debian.org
Fri Jan 19 10:23:09 UTC 2018
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository roary.
commit 80536c8d5a983b870a6d5124e8d4feb05de1c666
Author: Sascha Steinbiss <satta at debian.org>
Date: Mon Jan 15 13:40:19 2018 +0100
New upstream version 3.11.3+dfsg
---
README.md | 5 ++---
dist.ini | 2 +-
install_dependencies.sh | 2 +-
lib/Bio/Roary/CommandLine/Roary.pm | 17 +++++++++++++++--
lib/Bio/Roary/External/CheckTools.pm | 20 +++++++++++---------
lib/Bio/Roary/ExtractProteomeFromGFF.pm | 9 +++++++--
lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm | 7 ++++++-
7 files changed, 43 insertions(+), 19 deletions(-)
diff --git a/README.md b/README.md
index e65364c..823f49a 100644
--- a/README.md
+++ b/README.md
@@ -69,9 +69,8 @@ sudo cpanm -f Bio::Roary
```
## GNU Guix
-Roary is not included in version in [Guix](https://www.gnu.org/software/guix) 0.11.0 so `guix pull` is currently required before installation.
+Roary is included in [Guix](https://www.gnu.org/software/guix) and can be installed in the usual way:
```
-guix pull
guix package --install roary
```
@@ -130,7 +129,7 @@ The code will not work with perl 5.8 or below (pre-modern perl). We no longer te
* cdhit 4.6.1
* ncbi blast+ 2.4.0
* mcl 14-137
-* bedtools 2.26.0
+* bedtools 2.27.1
* prank 130410
* GNU parallel 20130922, 20160722, 20150122
* FastTree 2.1.9
diff --git a/dist.ini b/dist.ini
index e673cd7..1839c8f 100644
--- a/dist.ini
+++ b/dist.ini
@@ -3,7 +3,7 @@ author = Andrew J. Page <ap13 at sanger.ac.uk>
license = GPL_3
copyright_holder = Wellcome Trust Sanger Institute
copyright_year = 2013
-version = 3.11.0
+version = 3.11.3
main_module = lib/Bio/Roary.pm
[MetaResources]
diff --git a/install_dependencies.sh b/install_dependencies.sh
index 253ed7b..bdc0256 100755
--- a/install_dependencies.sh
+++ b/install_dependencies.sh
@@ -11,7 +11,7 @@ PARALLEL_VERSION=${PARALLEL_VERSION:-"20160722"}
PARALLEL_DOWNLOAD_FILENAME="parallel-${PARALLEL_VERSION}.tar.bz2"
PARALLEL_URL="http://ftp.gnu.org/gnu/parallel/${PARALLEL_DOWNLOAD_FILENAME}"
-BEDTOOLS_VERSION="2.26.0"
+BEDTOOLS_VERSION="2.27.1"
BEDTOOLS_DOWNLOAD_FILENAME="bedtools-${BEDTOOLS_VERSION}.tar.gz"
BEDTOOLS_URL="https://github.com/arq5x/bedtools2/releases/download/v${BEDTOOLS_VERSION}/${BEDTOOLS_DOWNLOAD_FILENAME}"
diff --git a/lib/Bio/Roary/CommandLine/Roary.pm b/lib/Bio/Roary/CommandLine/Roary.pm
index e2335a0..a98610c 100644
--- a/lib/Bio/Roary/CommandLine/Roary.pm
+++ b/lib/Bio/Roary/CommandLine/Roary.pm
@@ -21,6 +21,7 @@ use File::Which;
use File::Path qw(make_path);
use Cwd qw(abs_path getcwd);
use File::Temp;
+use File::Basename;
extends 'Bio::Roary::CommandLine::Common';
has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
@@ -120,7 +121,7 @@ sub BUILD {
Pubmed: 26198102\n\n";
$self->help($help) if ( defined($help) );
- if( $self->help )
+ if( $self->help )
{
print $self->usage_text;
return;
@@ -141,6 +142,18 @@ sub BUILD {
$self->logger->error("Error: You need to provide at least 2 files to build a pan genome");
die $self->usage_text;
}
+ my %basenames;
+ foreach my $string (@{$self->args}) {
+ my($base, $path, $suf) = fileparse($string);
+ next unless $basenames{$base}++;
+ $self->logger->error("Error: GFF files must have unique basenames.");
+ die $self->usage_text;
+ }
+
+ if ( @{ $self->args } < 2 ) {
+ $self->logger->error("Error: You need to provide at least 2 files to build a pan genome");
+ die $self->usage_text;
+ }
$self->output_filename($output_filename) if ( defined($output_filename) );
$self->job_runner($job_runner) if ( defined($job_runner) );
$self->makeblastdb_exec($makeblastdb_exec) if ( defined($makeblastdb_exec) );
@@ -246,7 +259,7 @@ sub _setup_output_directory {
sub run {
my ($self) = @_;
-
+
return if($self->version || $self->help);
$self->_setup_output_directory;
diff --git a/lib/Bio/Roary/External/CheckTools.pm b/lib/Bio/Roary/External/CheckTools.pm
index dc01fd5..1a73cf5 100644
--- a/lib/Bio/Roary/External/CheckTools.pm
+++ b/lib/Bio/Roary/External/CheckTools.pm
@@ -57,28 +57,30 @@ my %tools = (
},
'mafft' => {
GETVER => "mafft --version < /dev/null 2>&1",
- REGEXP => qr/(\d+\.\d+) /,
+ REGEXP => qr/(\d+\.\d+)/,
NEEDED => 1,
},
'kraken' => {
- GETVER => "kraken --version | head -n 1",
- REGEXP => qr/(\d+\.\d+\.\d+.*)/,
+ GETVER => "kraken -v | head -n 1",
+ REGEXP => qr/(\d+\.\d+\.*\d*.*)/,
NEEDED => 0,
},
'kraken-report' => {
- GETVER => "kraken-report --version | head -n 1",
- REGEXP => qr/(\d+\.\d+\.\d+.*)/,
+ GETVER => "kraken-report -v | head -n 1",
+ REGEXP => qr/(\d+\.\d+\.*\d*.*)/,
NEEDED => 0,
- },
+ },
'Rscript' => {
GETVER => "Rscript --version 2>&1 | head -n 1",
REGEXP => qr/R scripting front-end version ($BIDEC)/,
MINVER => "3",
NEEDED => 0,
},
-
- # prank version also performs an update check so cant use it
- 'prank' => { NEEDED => 0 },
+ 'prank' => {
+ GETVER => "prank | grep -m 1 ^prank",
+ REGEXP => qr/prank v.(\d+)/,
+ NEEDED => 0,
+ },
# now just the standard unix tools we need
'grep' => { NEEDED => 1 },
diff --git a/lib/Bio/Roary/ExtractProteomeFromGFF.pm b/lib/Bio/Roary/ExtractProteomeFromGFF.pm
index 8940aed..a96e087 100644
--- a/lib/Bio/Roary/ExtractProteomeFromGFF.pm
+++ b/lib/Bio/Roary/ExtractProteomeFromGFF.pm
@@ -132,8 +132,13 @@ sub _cleanup_fasta {
open( my $in, '<', $infile );
open( my $out, '>', $outfile );
while ( my $line = <$in> ) {
- chomp $line;
- $line =~ s/"//g if ( $line =~ /^>/ );
+ chomp $line;
+ if ( $line =~ /^>/ )
+ {
+ $line =~ s/"//g;
+ # newer versions of Bedtools add (-) or (+) to the end of the sequence name, remove them
+ $line =~ s!\([-+]\)!!;
+ }
if($line =~ /^(>[^:]+)/)
{
diff --git a/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm b/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm
index 14413dc..2a16b1a 100644
--- a/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm
+++ b/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm
@@ -177,7 +177,12 @@ sub _cleanup_fasta {
open( my $out, '>', $outfile );
while ( my $line = <$in> ) {
chomp $line;
- $line =~ s/"//g if ( $line =~ /^>/ );
+ if ( $line =~ /^>/ )
+ {
+ $line =~ s/"//g ;
+ # newer versions of Bedtools add (-) or (+) to the end of the sequence name, remove them
+ $line =~ s!\([-+]\)!!;
+ }
if($line =~ /^(>[^:]+)/)
{
--
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