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satta pushed a commit to branch upstream
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commit c94f09af9229b63920a1498583f191297614bd21
Author: Sascha Steinbiss <sa...@debian.org>
Date: Mon May 29 16:38:33 2017 +0200
New upstream version 3.8.2+dfsg
---
AUTHORS | 2 +-
README.md | 26 +++++++++++++-------------
dist.ini | 2 +-
lib/Bio/Roary.pm | 2 ++
lib/Bio/Roary/CommandLine/Roary.pm | 8 +++++++-
lib/Bio/Roary/External/Mcl.pm | 4 ++--
6 files changed, 26 insertions(+), 18 deletions(-)
diff --git a/AUTHORS b/AUTHORS
index f9d4e15..021f90a 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -1,2 +1,2 @@
Andrew J. Page (a...@sanger.ac.uk)
-Carla A. Cummins (c...@sanger.ac.uk)
+Carla A. Cummins (path-h...@sanger.ac.uk)
diff --git a/README.md b/README.md
index 5a4f94f..a0758a8 100644
--- a/README.md
+++ b/README.md
@@ -1,11 +1,11 @@
-#Roary the pan genome pipeline
+# Roary the pan genome pipeline
For instructions on how to use the software, the input format and output
formats, please see [the Roary
website](http://sanger-pathogens.github.io/Roary).
[](https://travis-ci.org/sanger-pathogens/Roary)
Roary is a high speed stand alone pan genome pipeline, which takes annotated
assemblies in GFF3 format (produced by Prokka) and calculates the pan genome.
Using a standard desktop PC, it can analyse datasets with thousands of samples,
something which is computationally infeasible with existing methods, without
compromising the quality of the results. 128 samples can be analysed in under
1 hour using 1 GB of RAM and a single processor. To perform this analysis using
existing methods wou [...]
-##Citation
+## Citation
"Roary: Rapid large-scale prokaryote pan genome analysis",
Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra
Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane,
Julian Parkhill,
Bioinformatics, (2015). doi:
http://dx.doi.org/10.1093/bioinformatics/btv421
@@ -23,13 +23,13 @@ Theres are a number of dependancies required for Roary,
with instructions specif
If the installation fails please contact your system administrator. If you
encounter a bug please let us know by emailing ro...@sanger.ac.uk .
-##Ubuntu/Debian
-###Debian Testing
+## Ubuntu/Debian
+### Debian Testing
```
sudo apt-get install roary
```
-###Ubuntu 14.04/16.04
+### Ubuntu 14.04/16.04
All the dependancies can be installed using apt and cpanm. Root permissions
are required. Ubuntu 16.04 contains a package for Roary but it is frozen at
v3.6.0.
```
@@ -37,13 +37,13 @@ sudo apt-get install bedtools cd-hit ncbi-blast+ mcl
parallel cpanminus prank ma
sudo cpanm -f Bio::Roary
```
-###Ubuntu 12.04
+### Ubuntu 12.04
Some of the software versions in apt are quite old so follow the instructions
for [LinuxBrew](http://brew.sh/linuxbrew/) below.
-##CentOS/RedHat
+## CentOS/RedHat
To install the dependancies, the easiest way is to install
[LinuxBrew](http://brew.sh/linuxbrew/) using the steps for Fedora, then follow
the steps below for installing Roary on LinuxBrew.
-##Homebrew/Linuxbrew - OSX/Linux
+## Homebrew/Linuxbrew - OSX/Linux
Assuming you have [homebrew](http://brew.sh/) (OSX) or
[linuxbrew](http://brew.sh/linuxbrew/) (Linux) setup and installed on your
system:
```
@@ -52,21 +52,21 @@ brew install bedtools cd-hit blast mcl parallel prank mafft
fasttree cpanm
sudo cpanm -f Bio::Roary
```
-##GNU Guix
+## 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.
```
guix pull
guix package --install roary
```
-##Virtual Machine - OSX/Linux/Windows
+## Virtual Machine - OSX/Linux/Windows
Roary wont run natively on Windows but we have created virtual machine which
has all of the software setup, including Prokka, along with the test datasets
from the paper. It is based on [Bio-Linux
8](http://environmentalomics.org/bio-linux/). You need to first install
[VirtualBox](https://www.virtualbox.org/), then load the virtual machine, using
the 'File -> Import Appliance' menu option. The root password is 'manager'.
ftp://ftp.sanger.ac.uk/pub/pathogens/pathogens-vm/pathogens-vm.latest.ova
More importantly though, if your trying to do bioinformatics on Windows, your
not going to get very far and you should seriously consider upgrading to Linux.
-##Docker - OSX/Linux/Windows/Cloud
+## Docker - OSX/Linux/Windows/Cloud
We have a docker container which gets automatically built from the latest
version of Roary in Debian Med. To install it:
```
@@ -78,7 +78,7 @@ To use it you would use a command such as this (substituting
in your directories
docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/roary roary -f
/data /data/*.gff
```
-##Installing from source (advanced Linux users only)
+## Installing from source (advanced Linux users only)
As a last resort you can install everything from source. This is for users
with advanced Linux skills and we do not provide any support with this method
since you have the skills to figure things out.
Download the latest software from
(https://github.com/sanger-pathogens/Roary/tarball/master).
@@ -109,7 +109,7 @@ bedtools cd-hit blast mcl GNUparallel prank mafft fasttree
## Ancient systems and versions of perl
The code will not work with perl 5.8 or below (pre-modern perl). We no longer
test against 5.10 (released 2007). If your running a very old verison of Linux,
your also in trouble.
-#Versions of software we test against
+# Versions of software we test against
* Perl 5.14, 5.16, 5.20, 5.24
* cdhit 4.6.1
* ncbi blast+ 2.4.0
diff --git a/dist.ini b/dist.ini
index bfcd266..5d2900f 100644
--- a/dist.ini
+++ b/dist.ini
@@ -1,5 +1,5 @@
name = Bio-Roary
-version = 3.8.0
+version = 3.8.2
author = Andrew J. Page <a...@sanger.ac.uk>
license = GPL_3
copyright_holder = Wellcome Trust Sanger Institute
diff --git a/lib/Bio/Roary.pm b/lib/Bio/Roary.pm
index 13a80d0..feccc74 100644
--- a/lib/Bio/Roary.pm
+++ b/lib/Bio/Roary.pm
@@ -47,6 +47,7 @@ has 'group_limit' => ( is => 'rw', isa =>
'Num', default =
has 'core_definition' => ( is => 'rw', isa => 'Num', default
=> 1.0 );
has 'verbose' => ( is => 'rw', isa => 'Bool', default
=> 0 );
has 'mafft' => ( is => 'ro', isa => 'Bool', default
=> 0 );
+has 'inflation_value' => ( is => 'rw', isa => 'Num', default
=> 1.5 );
has 'output_multifasta_files' => ( is => 'ro', isa => 'Bool', default => 0 );
@@ -108,6 +109,7 @@ sub run {
mcl_exec => $self->mcl_exec,
job_runner => $self->job_runner,
cpus => $self->cpus,
+ inflation_value => $self->inflation_value,
output_file => $output_mcl_filename
);
$mcl->run();
diff --git a/lib/Bio/Roary/CommandLine/Roary.pm
b/lib/Bio/Roary/CommandLine/Roary.pm
index f1a8ff1..8c8b0c8 100644
--- a/lib/Bio/Roary/CommandLine/Roary.pm
+++ b/lib/Bio/Roary/CommandLine/Roary.pm
@@ -54,6 +54,8 @@ has 'kraken_db' => ( is => 'rw', isa => 'Str', default =>
'/lustre/scratch118/i
has 'run_qc' => ( is => 'rw', isa => 'Bool', default => 0 );
has '_working_directory' => ( is => 'rw', isa => 'File::Temp::Dir', lazy => 1,
builder => '_build__working_directory' );
+has 'inflation_value' => ( is => 'rw', isa => 'Num', default
=> 1.5 );
+
sub _build__working_directory
{
my ($self) = @_;
@@ -69,7 +71,7 @@ sub BUILD {
$job_runner, $makeblastdb_exec, $mcxdeblast_exec,
$mcl_exec, $blastp_exec,
$apply_unknowns_filter, $cpus, $output_multifasta_files,
$verbose_stats, $translation_table,
$run_qc, $core_definition, $help,
$kraken_db, $cmd_version,
- $mafft, $output_directory, $check_dependancies,
+ $mafft, $output_directory, $check_dependancies,
$inflation_value,
);
GetOptionsFromArray(
@@ -99,6 +101,7 @@ sub BUILD {
'k|kraken_db=s' => \$kraken_db,
'w|version' => \$cmd_version,
'a|check_dependancies' => \$check_dependancies,
+ 'iv|inflation_value=f' => \$inflation_value,
'h|help' => \$help,
);
@@ -143,6 +146,7 @@ sub BUILD {
$self->mcxdeblast_exec($mcxdeblast_exec) if ( defined($mcxdeblast_exec)
);
$self->mcl_exec($mcl_exec) if ( defined($mcl_exec) );
$self->cpus($cpus) if ( defined($cpus) );
+ $self->inflation_value($inflation_value) if ( defined($inflation_value));
if ( defined($perc_identity) ) {
$self->perc_identity($perc_identity);
@@ -298,6 +302,7 @@ sub run {
core_definition => $self->core_definition,
verbose => $self->verbose,
mafft => $self->mafft,
+ inflation_value => $self->inflation_value,
);
$pan_genome_obj->run();
@@ -342,6 +347,7 @@ Options: -p INT number of threads [1]
-v verbose output to STDOUT
-w print version and exit
-y add gene inference information to spreadsheet, doesnt work
with -e
+ -iv STR Change the MCL inflation value [1.5]
-h this help message
Example: Quickly generate a core gene alignment using 8 threads
diff --git a/lib/Bio/Roary/External/Mcl.pm b/lib/Bio/Roary/External/Mcl.pm
index 7ae30d4..e86b366 100644
--- a/lib/Bio/Roary/External/Mcl.pm
+++ b/lib/Bio/Roary/External/Mcl.pm
@@ -31,7 +31,7 @@ has 'output_file' => ( is => 'ro', isa => 'Str', default
=> 'output_groups'
has '_score' => ( is => 'ro', isa => 'Str', default => 'r' );
-has '_inflation_value' => ( is => 'ro', isa => 'Num', default => 1.5 );
+has 'inflation_value' => ( is => 'ro', isa => 'Num', default => 1.5 );
has '_logging' => ( is => 'ro', isa => 'Str', default => '> /dev/null
2>&1' );
has 'memory_in_mb' => ( is => 'ro', isa => 'Int', lazy => 1, builder =>
'_build_memory_in_mb' );
@@ -84,7 +84,7 @@ sub _command_to_run {
$self->_full_mcxdeblast_exec, '-m9', '--score='.$self->_score,
'--line-mode=abc', $self->blast_results, '2> /dev/null',
'|', $self->mcl_exec, '-', '--abc',
- '-I', $self->_inflation_value, '-o', $self->output_file,
+ '-I', $self->inflation_value, '-o', $self->output_file,
$self->_logging
)
);
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